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Portable Testing Device IDs Covid-19 Variants

miSherlock device

Minimally instrumented Sherlock device (Wyss Institiute – Harvard Univ. and MIT)

6 Aug. 2021. A low-cost device is being developed that analyzes saliva samples for SARS-CoV-2 viral mutations, and returns results in about one hour. The device is the work of a team from the Wyss Institute for Biologically Inspired Engineering at Harvard University and Massachusetts Institute of Technology, and described in today’s issue of the journal Science Advances.

Since the start of the pandemic, the SARS-CoV-2 virus responsible for Covid-19 infections mutated into several variations, including the delta variant, now the dominant strain in the U.S. and other parts of the world. Most of today’s rapid tests for the SARS-CoV-2 virus are designed to detect the presence any SARS-CoV-2 virus, not specific variants. To identify those variants, nasal swab or other specimens must be genetically sequenced, which in most cases means sending a sample to a remote lab for analysis, with results returned many hours or days later.

Researchers from the biomedical engineering lab of James Collins, affiliated with the Wyss Institute and MIT, are seeking a fast, reliable, low-cost, and easy-to-use device to detect precise Covid-19 variants. The team of engineers and medical practitioners from Boston-area hospitals adapted a technology using the gene-editing technique Crispr, short for clustered regularly interspaced short palindromic repeats. Crispr is a genome-editing process based on bacterial defense mechanisms that use RNA to identify and monitor precise locations in DNA.

The researchers’ used an application of Crispr developed at the Broad Institute, affiliated with MIT and Harvard, called Sherlock, short for specific high-sensitivity enzymatic reporter unlocking. Sherlock uses Crispr editing enzymes that seek out specific genetic sequences in a specimen sample, and if detected in the sample, bind to and cut the RNA in nearby locations. Sherlock adds a reporter sequence to the RNA, a specific piece of synthetic RNA, which also gets cut by the editing enzyme, releasing a signal identifying the presence of the original target sequence. Those signals can be converted into a bioluminescent visual display that can appear on an everyday material like paper and at room temperature, or captured electronically.

High sensitivity and specificity

The battery-powered device, known as miSherlock, short for minimally instrumented Sherlock, captures an individual saliva sample, which is heated to 95 degrees C (203 F). After three to six minutes, the heated saliva sample is wicked into a filter, which the user transfers to a separate analysis chamber. The filter sample is pushed into the analysis chamber with a plunger that mixes the sample with stabilizing chemicals, dithiothreitol and egtazic acid, to prevent enzymes in saliva from damaging RNA in the sample. That RNA is then extracted through a membrane.

After extraction, the sample RNA is mixed with freeze-dried Crispr chemicals activated by water in sealed packets. After about 55 minutes, the user can view any change in color indicating the presence of SARS-Cov-2 viral RNA in the sample. The researchers tested the miSherlock device with saliva samples from 27 Covid-19 infected patients, and 21 healthy individuals, and compared the results to conventional RT-PCR tests for SARS-CoV-2. The results show miSherlock returns results with 96 percent true-positive sensitivity and 95 percent true-negative specificity. Further tests show the device can accurately detect the three known variants at the time: B.1.1.7, B.1.351, and P.1, now identified as alpha, beta, and gamma respectively. The team is extending the technology to also detect the delta variant.

A major advantage of miSherlock is its ease of manufacture, with a 3-D printer, and its low cost. The researchers say the device in the study costs $15.00 to produce, but by reusing some its parts, the cost can be lowered to $11.00. Mass production can reduce the unit cost further to as low as $3.00.

“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,” says Collins in a Wyss Institute statement, “so we pushed ourselves to create a truly decentralized, flexible, user-friendly diagnostic platform. By solving the sample prep problem, we’ve ensured that this device is virtually ready for consumers to use as-is, and we’re excited to work with industrial partners to make it commercially available.”

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