Fast, cheap test can detect COVID-19 virus' genome without need for PCR


Date:
January 24, 2022
Source:
University of Washington
Summary:
Researchers have developed a new test for COVID-19 that combines
the speed of over-the-counter antigen tests with the accuracy of
PCR tests that are processed in medical labs and hospitals.



FULL STORY ========================================================================== Researchers at the University of Washington have developed a new test
for COVID-19 that combines the speed of over-the-counter antigen tests
with the accuracy of PCR tests that are processed in medical labs and hospitals.


==========================================================================
The Harmony COVID-19 test is a diagnostic test that, like PCR tests
for COVID- 19, detects genetic material from the SARS-CoV-2 virus. But
whereas conventional PCR tests can take several hours, the Harmony kit
can provide results in less than 20 minutes for some samples and with
similar accuracy.

"We designed the test to be low-cost and simple enough that it
could be used anywhere," said Barry Lutz, a UW associate professor
of bioengineering and investigator with the Brotman Baty Institute for Precision Medicine. "We hope that the low cost will make high-performance testing more accessible locally and around the world." Lutz is senior
author on a paper published Dec. 15 in Science Advances that describes
the Harmony COVID-19 test kit. The researchers developed Harmony to be
simple and easy-to-use, employing ready-to-use reagents. The test uses a "PCR-like" method to detect the presence of the SARS-CoV-2 RNA genome in
a nasal swab sample with the aid of a small, low-cost detector, which
was also designed by Lutz's group. A smartphone is used to operate the
detector and read the results. The detector can handle up to four samples
at a time and would fit into a standard car's glove compartment.

The accuracy of COVID-19 tests has been a pressing matter throughout the pandemic. Many at-home antigen kits for COVID-19, which detect pieces
of the proteins the virus creates instead of its genetic material,
are 80-85% accurate, though accuracy may drop with the omicron variant,
which harbors a relatively high number of mutations not found in other
strains. PCR tests are generally 95% accurate or better -- a key FDA
benchmark -- but require expensive equipment and a long wait for results.

Initial results reported in the paper show that the Harmony kit is 97%
accurate for nasal swabs. The Harmony kit detects three different regions
of the virus' genome. If a new variant has many mutations in one region,
the new test can still detect the other two. It can, for example, detect
the omicron variant, which has dozens of mutations in the region of the
genome that encodes the so- called spike protein.



========================================================================== Though tests based on PCR -- or polymerase chain reaction -- are highly accurate, a key limitation is that PCR tests require dozens of cycles
of heating and cooling to detect genetic material in a sample. The
test developed by the UW team sidesteps this issue by relying on a
PCR-like method known as RT-LAMP, which doesn't have the same stringent temperature-cycling requirements.

"This test operates at a constant temperature, so it eliminates the time
to heat and cool and gives results in about 30 minutes," said Lutz.

Lutz and two colleagues spun out a new company from the UW, Anavasi Diagnostics, which last year was supported by $300,000 from WE-REACH and
later received $14.9 million in grants from the National Institutes of
Health to develop the Harmony prototype kit into a product and scale
up manufacturing to help address the ongoing shortage of COVID-19
diagnostic tests.

Initially, Lutz and his team hope the kits could be made available first
for use in clinics, as well as other settings with medical oversight,
such as workplaces and schools. Later, they would like to adapt the test
for home use.

"For a long time, the options have been either a PCR test that is
expensive and typically takes a day or more to get a result, or a rapid
antigen test that gives fast results and is low cost, but typically has
lower accuracy than a lab PCR test," said Lutz. "From the first day, we designed our test to be manufacturable at low cost and high volume, while delivering fast results with PCR-like performance." The NIH funding will support high-volume manufacturing at a new Anavasi facility near Seattle.

"We plan to make our test accessible and affordable throughout the world,"
said Lutz.

Lead author on the paper is Nuttada Panpradist, a recent UW doctoral alum
in bioengineering. Second author is Enos Kline, a UW research scientist
in bioengineering, who initiated the project in early 2020. Co-authors in
the Department of Bioengineering are doctoral students Robert Atkinson,
Ian Hull, Qin Wang, and Shane Gilligan-Steinberg; research scientists
Michael Roller, Jack Henry Kotnik, Crissa Bennett and Daniel Leon; and
doctoral alum Amy Oreskovic. Other co-authors, all at the UW, are Victoria
Lyon in the Department of Family Medicine; Matthew Thompson, a professor
of global health and the Helen D. Cohen Endowed Professor in Family
Medicine; Peter Han in the Department of Genome Sciences; Lea Starita,
an assistant professor of genome sciences; and Paul Drain, an associate professor of global health, of medicine and of epidemiology. The research
was funded by the Seattle Flu Study and the National Institutes of Health.

========================================================================== Story Source: Materials provided by University_of_Washington. Original
written by James Urton. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Nuttada Panpradist, Enos C. Kline, Robert G. Atkinson, Michael
Roller,
Qin Wang, Ian T. Hull, Jack H. Kotnik, Amy K. Oreskovic, Crissa
Bennett, Daniel Leon, Victoria Lyon, Shane D. Gilligan-Steinberg,
Peter D. Han, Paul K. Drain, Lea M. Starita, Matthew J. Thompson,
Barry R. Lutz.

Harmony COVID-19: A ready-to-use kit, low-cost detector, and
smartphone app for point-of-care SARS-CoV-2 RNA detection. Science
Advances, 2021; 7 (51) DOI: 10.1126/sciadv.abj1281 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/01/220124194941.htm

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