New at-home COVID test can detect specific variants in just an hour

A new at-home coronavirus test developed by scientists from the Massachusetts Institute of Technology (MIT), Harvard University and Boston-area hospitals can tell users within an hour if they’re infected with COVID and with what variant they’re infected.

Most at-home tests currently available are rapid antigen tests, which are not as reliable as the PCR tests available at official testing and healthcare centers. Testing for specific variants of the novel coronavirus is even less accessible, with a lack of global access to genetic testing causing delays in tracking and responding to new variants around the world.

Tracking variants has become a key element in the fight against the coronavirus pandemic, as new variants have been found to increase in infection as they mutate and can become more resistant to vaccines, with a recent Israeli study finding that the Pfizer coronavirus vaccine was only 40% effective against symptomatic cases of the virus.

“The ability to detect and track these variants is essential to effective public health, but unfortunately, variants are currently diagnosed only by nucleic acid sequencing at specialized epidemiological centers that are scarce even in resource-rich nations,” said Helena de Puig, a lead author on the study of the new device and a postdoc at Harvard University’s Wyss Institute for Biologically Inspired Engineering, according to MIT’s News Office.

The new Minimally Instrumented SHERLOCK (miSHERLOCK) device aims to fix these issues by providing an easy-to-use, affordable test that uses a saliva sample to test for the virus and specific variants and can be assembled using a 3D printer and commonly available components for about $15 (that price could drop to $2 or $3 if the device is mass-produced).

The scientists stressed that while saliva is not commonly used for coronavirus testing, several studies have shown that it is as reliable as nasal and mouth swabs. Israeli research published last month found that saliva tests performed similarly to swabs. SARS-CoV-19 has also been found to be detectable in saliva for a greater number of days after infection.

The miSHERLOCK device uses a CRISPR-based technology called “specific high sensitivity enzymatic reporter unlocking” (SHERLOCK), which was developed by Jim Collins, a senior paper author and core faculty member at Harvard University’s Wyss Institute for Biologically Inspired Engineering.

The SHERLOCK technology uses CRISPR’s “molecular scissors” to find viral RNA in saliva samples by snipping RNA or DNA at specific locations. The technology also cuts single-stranded DNA probes in order to produce a fluorescent signal.

The team needed to include a pre-processing step that disables enzymes called salivary nucleases, which destroy nucleic acids such as RNA, according to the MIT News Office. After the sample enters the device, the device uses heat and two chemical reagents to inactivate the nucleases. The viral RNA is then extracted and concentrated by passing the saliva through a membrane which traps RNA on its surface.

The battery-powered testing device is composed of two chambers: a heated sample preparation chamber and an unheated reaction chamber.

Using the testing device is an easy, three-step process. First, the user spits into the sample preparation chamber, turns on the heat and waits three to six minutes for the saliva to pass through the filter. The user then removes the filter and transfers it to the reaction chamber, pushes a plunger that deposits the filter into the chamber and punctures a water reservoir to activate the SHERLOCK reaction.

Less than an hour later, the user checks to make sure they can see a fluorescent signal through a window into the reaction chamber and can then use an accompanying smartphone app to analyze the pixels to provide a clear positive or negative diagnosis.

“Our goal was to create an entirely self-contained diagnostic that requires no other equipment,” said Xiao Tan, a clinical fellow at the Wyss Institute and an instructor in gastroenterology at Massachusetts General Hospital, to the MIT News Office. “Essentially the patient spits into this device, and then you push down a plunger and you get an answer an hour later.”

The device is modular and can hold up to four modules that each look for a different target RNA sequence. The original module includes RNA guide strands that detect any strain of the novel coronavirus, while the other modules can include guide strands to look for specific variants.

Co-first author Devora Najjar, a Research Assistant at the MIT Media Lab and in the Collins Lab, explained that modules for new variants could be created in about two weeks, which would allow for the rapid development of tests for new variants.

The device was tested on saliva samples from 27 COVID-19 patients and 21 healthy patients and correctly identified coronavirus-positive patients 96% of the time and coronavirus-negative patients 95% of the time, according to the Wyss Institute.

The device was also tested on its performance identifying the Alpha, Beta and Gamma variants of SARS-CoV-19 (the Delta variant was not widespread when the study began) and the device managed to effectively identify the variants.

“When the miSHERLOCK project started, there was almost no SARS-CoV-2 variant monitoring happening. We knew that variant tracking was going to be incredibly important when evaluating the long-term effects of COVID-19 on local and global communities, so we pushed ourselves to create a truly decentralized, flexible, user-friendly diagnostic platform,” said Collins in a press release by the Wyss Institute, stressing that the team is “excited to work with industrial partners to make it commercially available.”

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