New device can diagnose COVID-19 from saliva samples
The tabletop diagnostic yields results in an hour and can be programmed
to detect variants of the SARS-CoV-2 virus

Date:
August 6, 2021
Source:
Massachusetts Institute of Technology
Summary:
A new device can detect SARS-CoV-2 from saliva in about an hour.

Researchers report that the diagnostic is just as accurate as PCR
tests and can identify COVID-19 variants.



FULL STORY ========================================================================== Engineers at MIT and Harvard University have designed a small tabletop
device that can detect SARS-CoV-2 from a saliva sample in about an
hour. In a new study, they showed that the diagnostic is just as accurate
as the PCR tests now used.


==========================================================================
The device can also be used to detect specific viral mutations linked to
some of the SARS-CoV-2 variants that are now circulating. This result
can also be obtained within an hour, potentially making it much easier
to track different variants of the virus, especially in regions that
don't have access to genetic sequencing facilities.

"We demonstrated that our platform can be programmed to detect new
variants that emerge, and that we could repurpose it quite quickly,"
says 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 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." The new diagnostic, which relies on CRISPR technology, can
be assembled for about $15, but those costs could come down significantly
if the devices were produced at large scale, the researchers say.

Collins is the senior author of the new study, which appears today
in Science Advances. The paper's lead authors are Helena de Puig, a
postdoc at Harvard University's Wyss Institute for Biologically Inspired Engineering; Rose Lee, an instructor in pediatrics at Boston Children's Hospital and Beth Israel Deaconess Medical Center and a visiting fellow at
the Wyss Institute; Devora Najjar, a graduate student in MIT's Media Lab;
and Xiao Tan, a clinical fellow at the Wyss Institute and an instructor
in gastroenterology at Massachusetts General Hospital.

A self-contained diagnostic The new diagnostic is based on SHERLOCK,
a CRISPR-based tool that Collins and others first reported in
2017. Components of the system include an RNA guide strand that allows detection of specific target RNA sequences, 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.



==========================================================================
Last year, Collins' lab began working on adapting this technology to
detect the SARS-CoV-2 virus, hoping that they could design a diagnostic
device that could yield rapid results and be operated with little or no expertise. They also wanted it to work with saliva samples, making it
even easier for users.

To achieve that, the researchers had to incorporate a critical
pre-processing step that disables enzymes called salivary nucleases, which destroy nucleic acids such as RNA. Once the sample goes into the device,
the nucleases are inactivated by heat and two chemical reagents. Then,
viral RNA is extracted and concentrated by passing the saliva through
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.

This RNA sample is then exposed to freeze-dried CRISPR/Cas components,
which are activated by automated puncturing of sealed water packets
within the device. The one-pot reaction amplifies the RNA sample and
then detects the target RNA sequence, if present.

"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 researchers designed the device, which they call
minimally instrumented SHERLOCK (miSHERLOCK), so that it can have up to
four modules that each look for a different target RNA sequence. The
original module contains RNA guide strands that detect any strain of SARS-CoV-2. Other modules are specific to mutations associated with some
of the variants that have arisen in the past year, including B.1.1.7,
P.1, and B.1.351.



==========================================================================
The Delta variant was not yet widespread when the researchers performed
this study, but because the system is already built, they say it should
be straightforward to design a new module to detect that variant. The
system could also be easily programmed to monitor for new mutations that
could make the virus more infectious.

"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.

Tracking variants The researchers first tested their device with human
saliva spiked with synthetic SARS-CoV-2 RNA sequences, and then with
about 50 samples from patients who had tested positive for the virus. They found that the device was just as accurate as the gold standard PCR tests
now used, which require nasal swabs and take more time and significantly
more hardware and sample handling to yield results.

The device produces a fluorescent readout that can be seen with the naked
eye, and the researchers also designed a smartphone app that can read the results and send them to public health departments for easier tracking.

The researchers believe their device could be produced at a cost as low
as $2 to $3 per device. If approved by the FDA and manufactured at large
scale, they envision that this kind of diagnostic could be useful either
for people who want to be able to test at home, or in health care centers
in areas without widespread access to PCR testing or genetic sequencing
of SARS-CoV-2 variants.

"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," de Puig says.

The research was funded by the Wyss Institute; the Paul G. Allen Frontiers Group; the Harvard University Center for AIDS Research, which is supported
by the National Institutes of Health; a Burroughs-Wellcome American
Society of Tropical Medicine and Hygiene postdoctoral fellowship; an
American Gastroenterological Association Takeda Pharmaceutical Research
Scholar Award; and an MIT-TATA Center fellowship.

========================================================================== Story Source: Materials provided by
Massachusetts_Institute_of_Technology. Original written by Anne
Trafton. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Helena de Puig, Rose A. Lee, Devora Najjar, Xiao Tan, Luis
R. Soekensen,
Nicolaas M. Angenent-Mari, Nina M. Donghia, Nicole E. Weckman,
Audrey Ory, Carlos F. Ng, Peter Q. Nguyen, Angelo S. Mao, Thomas
C. Ferrante, Geoffrey Lansberry, Hani Sallum, James Niemi,
James J. Collins. Minimally instrumented SHERLOCK (miSHERLOCK)
for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and
emerging variants. Science Advances, 2021; 7 (32): eabh2944 DOI:
10.1126/sciadv.abh2944 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/08/210806155901.htm

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