CRISPR virus detection tool can test you for 169 viruses at once

Imagine a world where you can go to the doctor and actually find out what is making you sick.

For doctors, it’s often easy to tell if a patient is sick — they’re coughing, feverish, and feel like hell — but knowing what’s making them sick can be far trickier, requiring a bevy of time-consuming diagnostic tests.

Now, a team of researchers from the Broad Institute has created a virus detection tool that can test for nearly all viruses that commonly infect humans, at once, delivering same-day results.

While that alone is remarkable, the tool can also simultaneously test more than 1,000 patients for a single virus — a capability that could prove invaluable during a viral outbreak.

Virus Detection on a Chip

The researchers published a study on their virus detection tool, which they’ve dubbed CARMEN (Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids), in the journal Nature on April 29.

The tool consists of a rubber chip slightly larger than a smartphone, which contains tens of thousands of compartments called “microwells,” each of which can hold a pair of tiny droplets.

To use CARMEN for virus detection, a researcher first extracts genetic material from viruses in a patient sample (like a nose swab or urine). They then make copies of the genetic material, add a fluorescent dye to it, and split the mixture into droplets.

The tool can also simultaneously test more than 1,000 patients for a single virus.

Next, they add one of those droplets to each microwell along with a droplet of a detection mixture.

The detection mixture contains the CRISPR protein Cas13, which is programmed to hunt down a specific viral sequence. If it finds it, it produces a signal the researcher can detect using a fluorescence microscope.

Using just one CARMEN chip, a researcher could test 1,048 patients’ samples for a single virus or up to five patients’ samples for 169 viruses — that’s every human-associated virus with at least 10 published genome sequences.

The Broad team used all of those viruses to put their tool to the test, evaluating 58 samples from patients with a variety of known infections against the full panel.

They then compared the CARMEN results to those of an existing virus detection technique — known as “next-generation sequencing” — and found 99.7% agreement between the two tests.

Scaling Up Patient Diagnostics

The researchers do note that CARMEN has some limitations — the equipment it currently requires would make the tool hard to deploy in a doctor’s office, for example, or in a public venue for screening during a viral outbreak.

Still, the entire virus detection process — from the extraction of the genetic material through results — takes under eight hours. The technique decreases the costs of reagents needed for each test 300-fold, and the process of creating the chips is incredibly simple.

“The microwell chips are made like a stamp — it’s rubber poured over a mold,” researcher Cheri Ackerman said in a news release. “We’re easily able to replicate and share this technology with collaborators.”

The Broad team is now attempting to secure FDA approval for CARMEN so that it can be put to use detecting viruses in both individuals and entire populations.

“Imagine a world in which you go to the doctor and you actually find out which virus is making you sick,” researcher Catherine Freije told the Holland Sentinel.

“Instead of wondering what’s circulating in a community, we actually get stats,” she continued. “Real, good measurements of what’s there, how fast it’s spreading and what populations it’s circulating in.”

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