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Smartphone-based device could detect SARS-CoV-2

Researchers are developing a portable device that gives rapid, accurate test results with the help of a regular smartphone camera. By estimating the number of virus particles in samples, the device could also determine an infection’s progress.

A recent survey in the United States revealed that it takes an average of 4 days to receive a definitive SARS-CoV-2 lab test result after a nasal swab.

Lab-based tests are much more reliable than rapid, on-the-spot tests for SARS-CoV-2, the virus that causes COVID-19. They use a technique called polymerase chain reaction (PCR) to “amplify” the minuscule amounts of viral genetic material in a sample.

But the tests are time-consuming, increasing the risk of viral transmission while people wait for their results to come back from the lab.

The new test uses a different technology called CRISPR, which the researchers believe can reliably detect the RNA, or genetic material, of SARS-CoV-2 without amplifying it first.

This means that it is possible not only to detect the presence of the virus but also to estimate the number of virus particles, which is a good indicator of the infection’s progress.

CRISPR, which scientists principally use to edit genes, won the 2020 Nobel Prize in Chemistry for its creators, Emanuelle Charpentier and Jennifer A. Doudna.

About 2 years ago, Doudna, in collaboration with her colleagues at the J. David Gladstone Institutes in San Francisco, CA, began working on a new application for CRISPR to test for HIV.

In January 2020, as the global threat from the COVID-19 outbreak became apparent, they switched their focus to developing a test for SARS-CoV-2 using the same technology.

Their device, which is no bigger than a shoebox, employs a variation of CRISPR called CRISPR-Cas13a.

Cas13a is an enzyme that cleaves RNA molecules. By combining it with a strip of “guide RNA,” scientists can target it at a telltale sequence in a particular virus’s RNA.

The researchers use several guide RNAs that bind to different parts of the viral RNA to boost the test’s accuracy.

Binding to target sequences activates the enzyme, which then splits any RNA molecules in its vicinity.

To provide a visible signal that Cas13a has detected its target sequence, the researchers added an RNA-based probe to the mix. The probe emits fluorescent light when the activated enzyme splits it.

The detector comprises a laser to illuminate the sample and a lens to focus any fluorescent light produced. The phone’s camera, positioned over the lens, registers the intensity of the emitted light.

Using samples of SARS-CoV-2 RNA of varying concentrations, the researchers showed that the device could measure concentrations of as little as 100 virus particles per microliter within 30 minutes.

It took the device only 5 minutes to identify patient swabs that the scientists had spiked with SARS-CoV-2 RNA.

“Our study shows that we can do the detection part of this assay very quickly, making the measurement with mass-produced consumer electronics,” says Daniel Fletcher, a bioengineer at the University of California, Berkeley, and co-senior author of the paper. “We don’t need fancy laboratory equipment.”

The paper appears in the journal Cell.

The researchers still have some work to do before they have a fully working device.

To test whether the technology works in principle, they used pre-extracted viral RNA. They are currently working on a way for the device to release RNA from the virus in a single step.

However, their research so far suggests that the camera from an ordinary cell phone works particularly well as a molecular detector.

“One takeaway is that the phone camera is 10 times better than the plate reader in the lab,” says Melanie Ott, co-senior author of the paper and a virologist at Gladstone Institutes and the University of California, San Francisco.

Previously, Fletcher’s lab has helped develop phone-based devices to detect parasites in blood and other samples.

The researchers now hope to develop a cheap, portable device that pharmacies and drop-in clinics could use for rapid and accurate SARS-CoV-2 tests. It will probably have a built in cell phone camera.

Ultimately, they dream of developing a device for use at home that would detect not only SARS-CoV-2 but also other viruses, such as those that cause the common cold and flu.

In principle, it is possible to adapt any device that incorporates the same CRISPR technology to detect any virus.

The authors write:

“In the future, direct detection by Cas13a, as outlined here, could be quickly modified to target the next respiratory pathogen that emerges, hopefully in time to help curb global spread.”

They note that the current study only provides a “proof-of-concept” for using CRISPR and mobile phone technology to detect viruses. “Additional work will be necessary to fully translate this work to a widely available point-of-care device,” they write.

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