Engineers have designed a small tabletop device that can detect SARS-CoV-2 from a saliva sample in about an hour. The diagnostic is just as accurate as the PCR tests now used. The device can also be used to detect specific viral mutations linked to some of the SARS-CoV-2 variants that are now circulating. This result can also be obtained within an hour, potentially making it much easier to track different variants of the virus, especially in regions that don’t have access to genetic sequencing facilities.
The new diagnostic can be assembled for about $15 but those costs could come down significantly if the devices were produced at large scale.
The new diagnostic is based on SHERLOCK, a CRISPR-based tool. 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 molecular components can be freeze-dried for long-term storage and reactivated upon exposure to water.
The researchers incorporated 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.
The researchers designed the device, which they call minimally instrumented SHERLOCK (miSHERLOCK), so that it can have up to four modules that each look for a different target RNA sequence. The original module contains RNA guide strands that detect any strain of SARS-CoV-2. Other modules are specific to mutations associated with some of the variants that have arisen in the past year, including B.1.1.7, P.1, and B.1.351.
The Delta variant was not yet widespread when the researchers performed this study but because the system is already built, it should be straightforward to design a new module to detect that variant. The system could also be easily programmed to monitor for new mutations that could make the virus more infectious.
The researchers first tested their device with human saliva spiked with synthetic SARS-CoV-2 RNA sequences and then with about 50 samples from patients who had tested positive for the virus. They found that the device was just as accurate as the gold standard PCR tests now used, which require nasal swabs and take more time and significantly more hardware and sample handling to yield results.
The device produces a fluorescent readout that can be seen with the naked eye and the researchers also designed a smartphone app that can read the results and send them to public health departments for easier tracking. The researchers believe the device could be produced at a cost as low as $2 to $3 per device.