Scientists at Harvard and MIT have developed a low-cost, CRISPR-based diagnostic test that allows users to test themselves for the SARS-CoV-2 virus and its multiple variants using a saliva sample at home, with no extra instruments needed. The device, called minimally instrumented SHERLOCK (miSHERLOCK), is easy to use and provides results that can be read and verified on a smartphone app within one hour, the researchers said.
“It successfully distinguished between three different variants of SARS-CoV-2 in experiments, and can be rapidly reconfigured to detect additional variants like Delta,” they said.
The device, described in the journal Science Advances, 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.
“miSHERLOCK eliminates the need to transport patient samples to a centralised 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 Helena de Puig, a Postdoctoral Fellow at Harvard University and the Massachusetts Institute of Technology (MIT).
The researcher used a CRISPR-based technology called “specific high sensitivity enzymatic reporter unlocking” (SHERLOCK).
CRISPR technology is a simple yet powerful tool for editing genomes. It allows researchers to easily alter DNA sequences and modify gene function. SHERLOCK makes use of CRISPR’s molecular scissors — an enzyme called Cas12a — to snip DNA or RNA at specific locations.
The researchers used SHERLOCK 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 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. The spike protein is used by the SARS-CoV-2 virus to infect and enter the human cells.
The team used saliva rather than nasopharyngeal swab samples for the test 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. The researchers tested their diagnostic device using clinical saliva samples from 27 COVID-19 patients and 21 healthy patients.
They found that miSHERLOCK correctly identified COVID-19-positive patients 96 per cent of the time and patients without the disease 95 per cent of the time. The researchers 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.
They 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 Devora Najjar, a Research Assistant at the MIT Media Lab.
The team created their device with low-resource settings in mind, as the pandemic has brought to light the vast inequalities in healthcare access that exist between different parts of the world.