A Clarifi test kit, showing the swab and tube used to collect saliva.

How scientists created a top COVID-19 test that uses saliva

The process is cost-effective, easy and reliable

BY AMBER SMITH

In his career as a scientist, Frank Middleton, PhD, has developed saliva tests to diagnose autism, concussions and Parkinson’s disease.

The RNA found in saliva carries the genetic information for those conditions, but also for many viruses.

After the first coronavirus test kits from the U.S. Centers for Disease Control and Prevention were flawed, Middleton got to thinking: “We should build a better test. There’s no reason we couldn’t do this with saliva.”

He worked with Upstate faculty colleagues and people from Upstate’s Start Up New York business partner, Quadrant Biosciences, to create a way to test human saliva for the presence of the virus that causes COVID-19. The test, called Clarifi COVID-19, received authorization in September 2020.

Three months later, the U.S. Food and Drug Administration cited the Clarifi test as the No. 1 ranked saliva test in the United States and the sixth most sensitive worldwide in detecting the virus. New York Gov. Andrew Cuomo credits the test with helping State University of New York campuses pinpoint COVID-19 cases at early stages.

“This crucial development and expertise has played a critical role in ensuring SUNY students were tested efficiently and, if positive, isolated and on a path to recovery sooner,” Cuomo said.

The Clarifi test is different than other saliva-based tests that have FDA authorization because it stabilizes the RNA in the samples, allowing them to be transported to Upstate for testing. Also, the test deactivates the coronavirus, which allows lab workers to safely handle the samples.

Samples are collected using a swab, rather than requiring patients to spit. That leads to fewer false positive results.

Best at early detection

Middleton, who has a doctorate in neuroscience and also works in biochemistry and molecular biology, explains that the FDA reviews COVID-19 tests based on the effectiveness of finding the smallest traces of SARS-CoV-2, the virus that causes COVID-19. In the saliva testing category, Clarifi has the lowest limit of detection at 600 copies of the virus per milliliter. That means it’s the best at detecting infections at the earliest stages, when people may be infectious, but asymptomatic.

“Upstate Medical's and Quadrant Biosciences' saliva test is significant for SUNY – it’s not only fast and easy to use with results back within 48 hours, but also the test itself finds the virus within the earliest stages of the illness, so we can know who is positive more quickly and ensure they isolate from others,” SUNY Chancellor Jim Malatras said in praising the development.

The additional breakthrough of “pooled testing” has allowed Upstate to accelerate the process and expand testing capacity. Individuals use a swab to collect their own saliva. Lab technicians at Upstate combine from 10 to 25 samples into one pool for the COVID-19 test.

A negative result means everyone in the pool is presumed to be free of coronavirus.

A positive result means each individual sample in the pool needs to be tested again, individually, to pinpoint positive cases. This rapid retesting does not require people to submit new samples.

Upstate President Mantosh Dewan, MD, explained that pooled testing saves money. A single coronavirus test for an insured patient costs about $100. Pooled saliva testing drops that to about $25 per patient.

SUNY paid for five machines to process the tests in Middleton’s lab. Upstate invested money in equipment, chemicals and other materials to launch the testing program, and both Upstate and Quadrant Biosciences are paying the salaries of lab workers.

Dewan praises the collaboration as “a ringing endorsement of the excellence that can come from partnerships with industry and public academia.”