New CRISPR-based COVID-19 test uses smartphone cameras to detect viral RNA

Identifying and isolating people who may be contagious with the coronavirus is essential to limit the spread of the disease. But even months after the start of the pandemic, many patients still wait days to receive COVID-19 test results.

Scientists at UC Berkeley and Gladstone Institutes have developed a new CRISPR-based COVID-19 diagnostic test that, using a smartphone camera, can provide a positive or negative result in 15 to 30 minutes. Unlike many other tests available, this test also gives an estimate of the viral load or the number of viral particles in a sample, which can help doctors monitor the progression of a COVID-19 infection and estimate how much how contagious a patient can be.

“Monitoring the progress of a patient’s infection could help healthcare professionals estimate the stage of infection and predict, in real time, how long and how much time is likely to heal. time the individual needs to quarantine, ”said Daniel Fletcher, professor of bioengineering at Berkeley and one of the study’s leaders.

The diagnostic test requires a cell phone camera and a small handheld device. (Photo courtesy Daniel Fletcher)

The technique was designed in collaboration with Dr Melanie Ott, director of the Gladstone Institute of Virology, as well as Berkeley professor Jennifer Doudna, who is a principal investigator at Gladstone, president of the Innovative Genomics Institute and a researcher of the Howard Hughes Medical Institute. . Doudna recently won the 2020 Nobel Prize in Chemistry for co-discovering genome editing of CRISPR-Cas, the technology behind this work.

Most COVID-19 diagnostic tests rely on a method called PCR, short for polymerase chain reaction, which looks for pieces of SARS-CoV-2 viral RNA in a sample. These PCR tests work by first isolating the viral RNA, then converting the RNA to DNA, then “amplifying” the DNA segments – making many identical copies – so that the segments can be more easily detected. .

The new diagnostic test takes advantage of the CRISPR Cas13 protein, which directly binds and cleaves RNA segments. This eliminates the steps of DNA conversion and amplification and greatly reduces the time required to complete the analysis.

“One of the reasons we’re excited about CRISPR-based diagnostics is the potential for quick and accurate results at the point of need,” said Doudna. “This is especially useful in places where access to testing is limited or where frequent and rapid testing is required. This could remove many of the bottlenecks we’ve seen with COVID-19. “

In the assay, CRISPR Cas13 proteins are “programmed” to recognize segments of SARS-CoV-2 viral RNA, then combined with a probe that fluoresces when cleaved. When the Cas13 proteins are activated by viral RNA, they begin to cleave the fluorescent probe. Using a portable device, the resulting fluorescence can be measured by the smartphone camera. The rate at which fluorescence becomes brighter is related to the number of virus particles in the sample.

“Recent models of SARS-CoV-2 suggest that frequent testing with a rapid turnaround time is what we need to overcome the current pandemic,” said Ott. “We hope that with an increase in testing, we can start to reopen economies and protect the most vulnerable populations.”

Now that the CRISPR test has been developed for SARS-CoV-2, it could be modified to detect RNA segments from other viral diseases, like the common cold, the flu, or even the human immunodeficiency virus. The team is currently working to consolidate the test into a device that could be made available in clinics and other care settings and one day could even be used at home.

“The end goal is to have a personal device, like a cell phone, that can detect a range of different viral infections and quickly determine whether you have a cold, SARS-Cov-2 or the flu,” said Fletcher. “This possibility exists now and more collaboration between engineers, biologists and clinicians is needed to make it a reality.”