Low-Cost Tabletop Device Detects SARS-CoV-2 Variants from Saliva Sample in an Hour

It is easy to use and provides results that can be read and verified by an accompanying smartphone app within one hour. It successfully distinguished between three different variants of SARS-CoV-2 in experiments, and can be rapidly reconfigured to detect additional variants like Delta. The device can be assembled using a 3D printer and commonly available components for about USD 15, and re-using the hardware brings the cost of individual assays down to USD 6 each.

For the SARS-CoV-2 detection piece of their diagnostic, the researchers turned to a CRISPR-based technology created in the lab of Wyss Core Faculty member and senior paper author Jim Collins, Ph.D. called “specific high sensitivity enzymatic reporter unlocking” (SHERLOCK). SHERLOCK makes use of CRISPR’s “molecular scissors” to snip DNA or RNA at specific locations, with an added bonus: upon recognizing its target sequence, this specific type of scissors also cuts other pieces of DNA in the surrounding area, allowing it to be engineered to produce a signal indicating that the target has been successfully cut.

The researchers created a SHERLOCK reaction designed to cut SARS-CoV-2 RNA at a specific region of a gene called Nucleoprotein that is conserved across multiple variants of the virus. When the molecular scissors – an enzyme called Cas12a – successfully binds to and cuts the Nucleoprotein gene, single-stranded DNA probes are also cut, producing a fluorescent signal. They also created additional SHERLOCK assays designed to target a panel of viral mutations in Spike protein sequences that represent three SARS-CoV-2 genetic variants: Alpha, Beta, and Gamma.
Armed with assays that could reliably detect viral RNA within the accepted concentration range for FDA-authorized diagnostic tests, the team next focused their efforts on solving what is arguably the most difficult challenge in diagnostics: sample preparation. The team chose to use saliva rather than nasopharyngeal swab samples as their diagnostic source material, because it’s easier for users to collect saliva and studies have shown that SARS-CoV-2 is detectable in saliva for a greater number of days post-infection. But unprocessed saliva presents challenges of its own: it contains enzymes that degrade various molecules, producing a high rate of false positives.

The researchers developed a novel technique to solve that problem. First, they added two chemicals called DTT and EGTA to saliva and heated the sample to 95°C for three minutes, deactivated the enzymes producing the false positive signal from the untreated saliva and sliced open any viral particles. They then incorporated a porous membrane that was engineered to trap RNA on its surface, which could finally be added directly to the SHERLOCK reaction to generate a result.

To integrate the saliva sample preparation and the SHERLOCK reaction into one diagnostic, the team designed a simple battery-powered device with two chambers: a heated sample preparation chamber, and an unheated reaction chamber. A user spits into the sample preparation chamber, turns on the heat, and waits three to six minutes for the saliva to be wicked into the filter. The user removes the filter and transfers it to the reaction chamber column, then pushes a plunger that deposits the filter into the chamber and punctures a water reservoir to activate the SHERLOCK reaction. 55 minutes later, the user looks through the tinted transilluminator window into the reaction chamber and confirms the presence of a fluorescent signal. They can also use an accompanying smartphone app that analyzes the pixels being registered by the smartphone’s camera to provide a clear positive or negative diagnosis.

The researchers tested their diagnostic device using clinical saliva samples from 27 COVID-19 patients and 21 healthy patients, and found that miSHERLOCK correctly identified COVID-19-positive patients 96% of the time and patients without the disease 95% of the time. They also tested its performance against the Alpha, Beta, and Gamma SARS-CoV-2 variants by spiking healthy human saliva with full-length synthetic viral RNA containing mutations representing each variant, and found that the device was effective across a range of viral RNA concentrations.
“One of the great things about miSHERLOCK is that it’s entirely modular. The device itself is separate from the assays, so you can plug in different assays for the specific sequence of RNA or DNA you’re trying to detect,” said co-first author Devora Najjar, a Research Assistant at the MIT Media Lab and in the Collins Lab. “The device costs about $15, but mass production would bring the housing costs down to about $3. Assays for new targets can be created in about two weeks, enabling the rapid development of tests for new variants of SARS-CoV-2 as well as for other infectious diseases.”

“miSHERLOCK eliminates the need to transport patient samples to a centralized testing location and greatly simplifies the sample preparation steps, giving patients and doctors a faster, more accurate picture of individual and community health, which is critical during an evolving pandemic,” said co-first author Helena de Puig, Ph.D., a Postdoctoral Fellow at the Wyss Institute and MIT.

Related Links:

Wyss Institute for Biologically Inspired Engineering at Harvard University
Massachusetts Institute of Technology