The new CRISPR-based COVID-19 test uses smartphone cameras to detect the virus’ RNA

Identifying and isolating people who may be contagious with the coronavirus is key to limiting the spread of the disease. But even months into the pandemic, many patients are still waiting days to receive COVID-19 test results.

Scientists from UC Berkeley and the Gladstone Institutes have developed a new CRISPR-based COVID-19 diagnostic test that, with the help of a smartphone camera, can provide a positive or negative result in 15 to 30 minutes. Unlike many other tests available, this test also provides 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 a patient it could be contagious.

“Monitoring the course of a patient’s infection could help healthcare professionals estimate the stage of infection and predict, in real time, how much time is likely to be needed for recovery and how long the individual should be quarantined.” , said Daniel Fletcher, a professor of bioengineering at Berkeley and one of the leaders of the study.

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

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

The new diagnostic test uses the CRISPR Cas13 protein, which directly binds and cleaves segments of RNA. This eliminates the DNA conversion and amplification steps 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 fast, accurate results when needed,” Doudna said. “This is particularly useful in places with limited access to testing or when frequent and rapid testing is needed. It could eliminate many of the bottlenecks we’ve seen with COVID-19. “

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

“Recent SARS-CoV-2 models suggest that frequent testing with fast response times is what we need to overcome the current pandemic,” said Ott. “Hopefully with more testing, we can begin to reopen economies and protect the most vulnerable populations “.

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

“The ultimate goal is to have a personal device, such as a cell phone, that is able to detect a range of different viral infections and quickly determine if you have a common cold or SARS-Cov-2 or flu,” he said. said Fletcher. “This possibility now exists and further collaboration between engineers, biologists and doctors is needed to make it happen.”