SOUTH KINGSTOWN, R.I. — Dr. Angela Slitt was already thinking about surveillance tools for COVID-19 before a single case was identified in Rhode Island.
In the beginning days of the pandemic, she monitored the challenges of the common polymerase chain reaction (PCR) tests; how access was severely hampered due to disruptions in the supply chain, how they required extraction of the nucleic acids, access to thermocyclers, and other lab equipment that was both sophisticated and expensive.
She knew there had to be another way, and one that she could help lead.
As soon as Rhode Island confirmed its first coronavirus case on March 1, 2020, Slitt, a professor of biomedical and pharmaceutical sciences at the University of Rhode Island, called Thermo Fisher Scientific, a Massachusetts-based laboratory equipment firm, to work with her.
A year later, Slitt and her team have developed a new saliva-based COVID-19 test that overcomes the challenges of PCR tests. This new test, called quantiCOVID-19, is not only less invasive than the nasal swabs that most tests use, but is sensitive, specific, eliminates the supply chain issues, and can deliver results at a lower cost with minimal scientific equipment.
“At first, I felt like I didn’t know where this would land, but wanted to create something that can be cheap and accessible because we still don’t know if the coronavirus would decimate some underdeveloped countries,” Slitt told the Globe.
Slitt was already using her research in URI’s Sources, Transport, Exposure, and Effects of PFASs (STEEP) lab to look at changes in genetic material. Her PFAS test is used to look at these changes using branched DNA assay technology, which is more commonly found in labs throughout the United States, and reasoned that this research could be adapted to identify coronavirus in saliva samples.
Thermo Fisher validated the team’s test and will provide the supply chain for distribution. Bio-Techne helped in the design, and URI invested approximately $300,000 toward the effort.
URI tests its thousands of students at least every two weeks using PCR tests, which costs the university about $25 per test. Student athletes and coaches are sometimes tested as frequently as three times a week. But Slitt’s saliva-based test slices that price in half; the university pays approximately $12.50 to run each quantiCOVID-19 test, according to Dr. Peter Snyder, URI’s vice president for research and economic development.
On Sunday, 500 student athletes at URI will begin getting tested each week using quantiCOVID-19, with a goal of administering 20,000 tests by the end of the semester.
Not only will this more affordable test help increase the university’s capacity for testing, but it’s also serving as the tests’ clinical trial, which is the final phase of data collection and validation in preparation for the university’s Emergency Use Authorization submission to the US Food and Drug Administration.
Though states are expanding access to the COVID-19 vaccine and trying to accelerate the rollout, Slitt and her team acknowledge that not everyone who is eligible will opt to get vaccinated. Variants of the coronavirus have been identified in Rhode Island, and it’s still unclear whether vaccines will be effective against these variants or how long those who have been vaccinate retain immunity. Testing for COVID-19 will likely remain important in the future.
“Every time that we think we have the virus under control, something changes. There’s so many variables and this is a tool. And I really don’t think we can have enough tools in our arsenal right now,” said Slitt.
Snyder said if quantiCOVID-19 receives emergency use authorization, the cost of each test could drop below $10.
“I realize that there are rapid tests on the market for less than that, but frankly it’s a sensitivity issue. This test is far more sensitive than the rapid tests,” said Snyder.
While PCR tests are considered the most-sensitive COVID-19 tests — they correctly identify nearly all people who are infected — all samples have to be processed with expensive lab equipment. Early on during the pandemic, results could take up to a week or more. This time frame has significantly decreased; in Rhode Island, results are usually ready in about one or two days.
The BinaxNOW rapid tests, which are also available in the state, offer results in approximately 15 minutes, but are not always accurate.
Slitt said this quantiCOVID-19 could be the answer.
BinaxNOW rapid tests detects SARS-CoV-2 viral RNA 40,000 copies per milliliter compared to “gold standard” PCR tests, which detects for 50 to 10,000 viral RNA copies per milliliter. But the quantiCOVID-19 test detects for a range of 3,000 to 5,000 viral RNA copies per milliliter, making it more accurate than the BinaxNOW test, though not as fast — results from the quantiCOVID-19 test are ready in 24 hours now, but Slitt said she is working on developing a shorter protocol so results take just eight hours.
The FDA in September 2020 authorized emergency use for SalivaDirect, a saliva test for COVID-19 developed by researchers at the Yale School of Public Health. That test detects for 18,000 viral RNA copies per milliliter, which is makes it likely to be less sensitive than quantiCOVID-19 tests.
Slitt presented the quantiCOVID-19 test to Dr. Deborah Birx, former coordinator of the White House Coronavirus Task Force, when Birx visited URI last fall.
“It’s a very promising test,” said Birx at the time. “What’s exciting is it works outside of the PCR platform using different reagents that will make the test more applicable, not only here, but potentially across the globe.”
Slitt said she will be submitting the tests for emergency use authorization in the next four to six weeks. If approved, it will be one of the few assay tests that could be made available globally, and could have a credible impact.