Low-cost device engineered for 1 hour Covid variant test

Harvard and MIT researchers have teamed up to prototype a self-contained saliva-based diagnostic Covid test that can distinguish between variants in an hour and is “just as accurate as the PCR tests now used”, according to MIT.

It is called ‘miSherlock’, for ‘minimally-instrumented Sherlock’, where Sherlock is a Crispr-based DNA/RNA test invented at Harvard’s Wyss Institute for Biologically Inspired Engineering.

Two parts are required: pre-packaged chemicals and reusable hardware consisting of common electronic components and 3d printed parts. On top of this, there is an optional phone app.

According to the Wyss Institute, the device can be assembled for ~$15 (~$3 mass-produced), and test should cost around $6 each.

“One of the great things about miSherlock is that it’s entirely modular,” said MIT researcher Devora Najjar. “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. Assays for new targets can be created in about two weeks, enabling the development of tests for new variants of SARS-CoV-2 as well as for other infectious diseases.”

There are several stages to the chemical assay (see below), and the hardware has been designed to turn these into simple steps for the user, who first spits into a custom container through a small disposable funnel.

The saliva container is pushed into the first of two chambers in the battery-powered hardware, where the sample is heated to 95°C for three to six minutes while it reacts and soaks into a filter.

It is this filter that goes into the second chamber, pushed in by the user with a plunger that also punctures a water reservoir, causing dried Sherlock chemicals to react with particles on the filter’s surface. Several tests can be done in the second chamber at the same time.

An in-built LED activated 55 minutes later causes the liquid to fluoresce noticeably if it contained Covid-19 or the specific variant of Covid-19 sought by the chemical package. The user “can also use an accompanying smartphone app that analyses the pixels being registered by the smartphone’s camera to provide a clear positive or negative diagnosis,” according to the Wyss Institute.

The bio-chemistry

Sherlock (specific high sensitivity enzymatic reporter unlocking) uses Crispr’s ‘molecular scissor’ action to snip DNA or RNA at a specific location, then does a second task if the first was successful

For this test, a Sherlock reaction was first designed as a blanket test to identify a segment of Covid-19 RNA shared by multiple variants, and then to cause a fluorescence if that was successful.

Subsequent Sherlock reactions were designed to detect Alpha, Beta and Gamma (Delta was rare during the project) mutations in the Covid-19 ‘spike’ protein separately, similarly indicating any detection with fluorescence.

Saliva is easy to collect compared with nose swabs, which is why it was chosen, according to the Institute, but saliva also has enzymes that cause false positives to be indicated.

The heating step activates chemicals in the sample container that halt these false-positive enzymes, as well as chemicals that break open any Covid-19 virus particles so that virus RNA can be trapped on the surface of the specially-designed filter.

Tested on 27 Covid-19 patients and 21 healthy patients, according to Harvard, the blanket version of miSherlock identified 96% of Covid-19 patients and 95% of healthy patients. The Alpha, Beta and Gamma distinguishing version of the test worked on artificial samples made from healthy saliva and synthetic viral RNA at a range of concentrations.

miSherlock is described in ‘Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants‘, published in Science Advances, and viewable without payment.