Engineers Discover New Device That Can Diagnose COVID-19 Variants From Saliva Samples

A new study has helped Engineers at MIT and Harvard University develop a little table top device that would be useful in detecting SARS-CoV-2 from samples of saliva within the hour. The team at MIT and Harvard were able to successfully show that diagnostic is just a s accurate as the PCR tests.

The research funded by the Wyss Institute; the Paul G. Allen Frontiers Group; the Harvard University Centre for AIDS Research and other firms designed the table top device to be able to detect specific viral mutations that have been linked to some of the now circulating SARS-CoV-2 variants. The result of the test can be gotten in an hour, having the potential of easier tracking of different variants of the virus, most especially in areas and regions that do not have access to genetic sequencing facilities.

James Collins, the Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering in his words said:

“We demonstrated that our platform can be programmed to detect new variants that emerge, and that we could repurpose it quite quickly. In this study, we targeted the U.K., South African, and Brazilian variants, but you could readily adapt the diagnostic platform to address the Delta variant and other ones that are emerging.”

According to the researchers, the  CRISPR technology relying diagnostic can be made with $15 with the tendency of the cost coming down if the devices are produced on a larger and wholesome scale,

The self-contained new diagnostic is crated on a SHERLOCK, a CRISPR-based tool that included an RNA guide strand which allows RNA sequences detection and Cas enzymes that cleave those sequences and produce a fluorescent signal. All of these molecular components can be freeze-dried for long-term storage and reactivated upon exposure to water.

Collins and his team had last year started work in the adaptation of the technology to help detect SARS-CoV-2 virus,  with the mandate of designing a diagnostic device that would be operated with little or no expertise and yet have rapid and effective results. To make it easier for users, they decided to work with saliva samples by incorporating a critical pre-processing step that would help in disabling salivary nucleases enzymes that destroys nucleic acids like RNA. With the samples going into the device, the nucleases are in sleep mode and thus inactivated by hear and two chemical reagents. In the process, viral RNA is extracted is taken out and concentrated with the passage of saliva via a membrane.

 “That membrane was key to collecting the nucleic acids and concentrating them so that we can get the sensitivity that we are showing with this diagnostic,” Lee says.

The ensuing RNA sample is exposed to activated CRISPR components with the one-pot reaction amplifying the RNA sample and the target RNA sequence if present is detected. It is of note that the CRISPr/Cas components are activated by the automated process of puncturing sealed water packets in the device.

 “Our goal was to create an entirely self-contained diagnostic that requires no other equipment,” Tan says. “Essentially the patient spits into this device, and then you push down a plunger and you get an answer an hour later.”

The coined SHERLOCK (miSHERLOCK) designed device from the researchers can have up to four modules that allows each of them look for a different target RNA sequence, with the original module containing RNA guide strands that can detect strains of SARS-CoV-2.

 “If you want to do more of a broad epidemiological survey, you can design assays before a mutation of concern appears in a population, to monitor for potentially dangerous mutations in the spike protein,” Najjar says.

In tracking variants, the researchers had their first device test with human saliva mixed with synthetic SARS-CoV-2 RNA sequences, together with about 50 samples from patients who have the virus. It was discovered that the device was just as accurate as the currently used PCR tests, that had hitherto required nasal swabs, and had taken more time, and sample handling to achieve results.

“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 centres that are scarce even in resource-rich nations,” de Puig says.

Reference; 6 August 2021, Science Advances.
DOI: 10.1126/sciadv.abh2944