Chesterton Tribune

 

 

CHS grad Doug Brackney a player in NBA funded saliva test research

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By KEVIN NEVERS

Dr. Doug Brackney, a 1997 Chesterton High School graduate and virologist by trade, has already made his bones in the cutting edge of COVID-19 research, by demonstrating in the spring--as part of a Yale University team--that high concentrations of coronavirus RNA in primary municipal sewer sludge are an excellent early warning sign of an impending community outbreak of C-19.

Brackney, however, has had more than one iron in the fire, and now an inexpensive and scalable saliva test for COVID-19 which he helped to develop, with another Yale team, has recently received emergency use authorization by the U.S. Food and Drug Administration.

Brackney isn’t actually Yale faculty. He’s an associate scientist at the Connecticut Agricultural Experiment Station studying virus-vectors, arthropods like mosquitoes, fleas, and ticks which transmit pathogens to animals. Brackney wrote his dissertation at Colorado State University on the dengue virus, did a post-doc at the University of New Mexico on the West Nile virus, and was happily ensconced in his lab with his critters when the pandemic forced its closure as “non-essential.”

Unwilling to cool his heels during lockdown, and possessed of a skill set he thought might be useful, Brackney made contact with a colleague at Yale and soon found himself tasked to the sewer sludge study but also to another project: this one to assess the feasibility of supplementing the ubiquitous nasopharyngeal test with something less clunky.

As Brackney told the Chesterton Tribune, the commonly used nasopharyngeal test--the insertion, that is, of a swab into the back of the nostril--is at once an invasive procedure and a complicated one. It requires a skilled healthcare worker to administer, a certified swab, a certified collection receptacle to deposit the swab in, and then a CLIA (Clinical Laboratory Improvement Amendments) lab to process the sample using both a PCR assay and an RNA extraction kit specifically approved by the FDA.

In short, the nasopharyngeal test involves a multitude of moving parts: parts, more to the point, which can only be sourced from particular vendors selling them often at a significant markup.

“This leads to supply-chain bottlenecks,” Brackney said. And, he added, to “profiteering and price-gouging.” Thus a certified swab which costs only $1 is suddenly being sold for $2 or $5.

So Nathan Grubaugh and Anne Wyllie at Yale’s School of Public Health wondered whether a saliva test--routinely used in the diagnosis of respiratory infections--could be developed as an alternative to the nasopharyngeal test, not only to uncomplicate the process, on the one hand, but also to free it from the grip of market forces, on the other.

The most important first step: to determine whether the coronavirus could be detected in saliva. Brackey, working with Willey, found that the virus could indeed be detected in saliva, that saliva in fact is “just as sensitive if not more sensitive than the swab test for COVID-19,” Brackney said.

The next step, and here Brackney brought his own expertise to bear: to develop a simpler PCR assay than the one originally approved by the CDC, which requires three separate reactions. “Our goal was to combine them into a single reaction and reduce the cost,” Brackney said. “We were able to do that. We showed we could condense it and get just as sensitive a result.”

Finally, the team wanted to remove one of the moving parts from the process altogether, by eliminating the need for RNA extraction, which requires a particular--and very expensive--kit. Brackney, accordingly, developed a way to bypass RNA extraction entirely, by treating a saliva sample with an enzyme and then placing the sample directly into a PCR assay. "It’s not quite as sensitive as full RNA extraction,” he said, “but it’s still very sensitive and can identify most infected individuals. It’s streamlined, cost-effective, and can easily be implemented in community-wide screening. We were willing to sacrifice a little sensitivity to be able to test people on scale.”

To be clear, what the team finally submitted to the FDA for emergency use authorization wasn’t so much a saliva test per se as a protocol for testing saliva, in which the method for processing the saliva is more important than the materials and instruments used in the processing. The latter can be swapped out, interchanged, and price-compared. “We tried to use products from as many different vendors as possible,” Brackney noted. “We used different PCR machines and master mixes and different enzymes.”

That protocol the team trademarked as SalivaDirect, Brackney said, and within a week of its receiving emergency use authorization from the FDA “we received 1,200 requests from labs wanting to get the protocol.” There is one condition, though, on which the Yale team insisted: for-profit labs may use the protocol, so long as they “agree not to hike up the price.”

Which is pretty nearly nominal: $1.30 to $4 per test, Brackney said, depending on what the vendors are charging for reagents. That compares to around $10 per for other tests, a 50- to 80-percent cost savings. “That was the whole idea: to make it more accessible and cheaper to use.”

A side note to the SalivaDirect research: much of it was funded by the National Basketball Association. “We partnered with the NBA as they were getting ready to go in the Bubble,” Brackney said. “We wanted to see how SalivaDirect compared to nasal swabs. We found a very high correlation between our results and the gold standard’s. In addition, both the asymptomatic and presymptomatic results were good. So it looks encouraging.”

Meanwhile, the Yale team continues what Brackney called “bridge studies,” in preparation for submitting SalivaDirect to the FDA for further approvals. But Brackney himself has returned to his own work on virus-vectors at the Connecticut Agricultural Experiment Station, which is now operating at 50-percent capacity. “The research was exciting and hopefully it’s making an impact,” he said. “And I’m glad I could help.”

 

Posted 10/1/2020

 
 
 
 

 

 

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