CRISPR device detects COVID variants in saliva

Written by: Andrew Wade | Published:
(Credit: Devora Najjar)

Scientists in the US have developed a compact CRISPR-based device to detect the presence of COVID in saliva and also identify specific variants of the virus.

Engineered in a joint project between MIT and Harvard, the $15 platform is claimed to be as accurate as the leading PCR tests available today and deliver results within an hour. Despite applying CRISPR technology, it does not require genetic sequencing facilities, making it ideal for more rural and remote regions. The work is published in Science Advances.

“We demonstrated that our platform can be programmed to detect new variants that emerge, and that we could repurpose it quite quickly,” said James Collins, a professor at MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering.

“In this study, we targeted the UK, South African, and Brazilian variants, but you could readily adapt the diagnostic platform to address the Delta variant and other ones that are emerging.”

The new device is based on SHERLOCK, a CRISPR-based tool that Collins and others first reported in 2017. Components of the system include an RNA guide strand that allows detection of specific target RNA sequences and Cas enzymes that cleave those sequences and produce a fluorescent signal. All of these molecular components can be freeze-dried for long-term storage and reactivated upon exposure to water.

To adapt this technology to work with saliva samples, the team had to incorporate a critical pre-processing step that disables enzymes called salivary nucleases, which destroy nucleic acids such as RNA. Once the sample goes into the device, the nucleases are inactivated by heat and two chemical reagents. Then, viral RNA is extracted and concentrated by passing the saliva through a membrane.

This RNA sample is then exposed to freeze-dried CRISPR/Cas components, which are activated by automated puncturing of sealed water packets within the device. The one-pot reaction amplifies the RNA sample and then detects the target RNA sequence, if present.

“Our goal was to create an entirely self-contained diagnostic that requires no other equipment,” said Xiao Tan, a clinical fellow at Harvard’s Wyss Institute. “Essentially the patient spits into this device, and then you push down a plunger and you get an answer an hour later.”

The researchers believe their device could be produced at a cost as low as $2 to $3 per unit. If given regulatory approval and manufactured at scale, they envision it could be useful either for people who want to be able to test at home, or in regions without widespread access to PCR testing or genetic sequencing of COVID variants.

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