Saliva Test for COVID-19: Researchers Enable Alternative to Nasal Swabs

Saliva samples instead of deep, “brain-tickling” nasal swabs: A new wave of noninvasive, less tech-intensive testing is the latest advance in the battle against COVID-19. Dedicated researchers like Anne Wyllie and Andrew Berglund are making it possible.

The need couldn’t be more urgent. University students are taking virtual classes yet moving back on campus. Professional athletes have been sequestered to bubbles and are playing their sports in front of zero live fans.

Preventing the spread of COVID-19 among healthy people living and working in close quarters is tricky. Saliva testing may represent the newest hope for staying ahead of the novel coronavirus.

[Read: Montana Physician Truly Heads Toward the Fire.]

Saliva in the Spotlight

Anne Wyllie, an associate research scientist at Yale School of Public Health in New Haven, Connecticut, has been studying saliva for the past 10 years. But she never expected the fruits of her research to draw attention from a professional sports league reacting to a global pandemic.

In late June, Yale announced a partnership with the National Basketball Association and the National Basketball Players Association to launch a study for testing players, coaches and staff with both standard nasal swab testing and Yale’s newly devised saliva approach, and then comparing the results for accuracy. They wanted to see if the saliva test could be as effective as the nasal swab route.

“This whole pandemic, just so many bizarre things have happened,” Wyllie says. “It’s been like putting one fire out after another. But the NBA was completely unexpected.”

Early on, COVID-19 testing using nasal swabs became the standard for most testing labs. But compared to saliva, nasal swab testing is relatively high-tech for labs to run — and uncomfortable for those being tested.

With SalivaDirect, the testing protocol developed by Wyllie and her Yale colleagues, labs can eliminate a cumbersome processing step. Instead of having to extract viral RNA material from a nasal swab sample, lab workers mix the saliva sample with a simple chemical reagent. Heating the mixture releases the virus particles.

On Aug. 4, the Yale team released preprint findings on its saliva-testing approach. The Yale researchers found more than 90% agreement between nasal swab and saliva testing results. Preprint articles are shared publicly before they have been peer-reviewed and so require further scientific evaluation.

However, the new method demonstrated potential to meet the nationwide need for inexpensive, accessible testing. On Aug. 15, the Food and Drug Administration issued an emergency use authorization for SalivaDirect, to allow wider use of the method.

Wyllie was in her lab when she got the message about the FDA announcement. “I was just sitting here alone, already working on that Saturday morning,” she says. “The enormity of it sort of dawned on me and I had a little quiet moment.” But she didn’t have the luxury of time for dwelling. “I dived back into work. There was just so much to do,” says Wyllie, whose previous saliva-related research includes other infectious organisms like pneumonia-causing bacteria.

As it was, a sense of urgency had sent the research team into overdrive. “We were already in the middle of the pandemic,” Wyllie says. “We’ve been working 8 a.m. to midnight, if not longer, almost seven days a week, regardless of what we were finding. We were working to respond to this.”

Depending on factors including chemical reagent costs, shipping of samples, testing equipment and personnel, labs could be charging anywhere from about $15 to $35 per saliva testing kit, Wyllie says.

That could represent significant savings if the method becomes widespread. “Our main motivation was this: We need tests to be affordable to everyone,” Wyllie says. “There’s no reason they need to be $100 or $150. We just wanted a test that could be would be more accessible to all communities across the country and not just those that could pay for it.”

[Read: Hospital Interpreter: We ‘Can Be the Difference Between Life and Death’.]

On Aug. 24, to the consternation of many health experts, the Centers for Disease Control and Prevention scaled back its recommendations on COVID-19 testing for people who don’t have symptoms. The CDC now advises that you do not need a test if you’re asymptomatic and have not been in close contact with someone known to have a COVID-19 infection. On Aug. 26, CDC director Dr. Robert Redfield clarified the message with a statement that testing “may be considered” for asymptomatic contacts of people with confirmed or probable cases of COVID-19.

Because asymptomatic spread is thought to be a key driver of COVID-19 infection, many organizations are moving in the opposite direction — ramping up COVID-19 testing to identify cases among seemingly healthy people, to prevent the spread of the coronavirus and stave off disastrous outbreaks among those under their responsibility.

Saliva Surveillance Pools

Andrew Berglund, director of the RNA Institute at the University at Albany in New York, has devoted much of his career to studying myotonic dystrophy, a common form of muscular dystrophy. But in 2020 his laboratory made a sharp pivot to pandemic work — developing pooled saliva testing to allow widespread COVID-19 surveillance among university students, faculty and staff. Pooled testing allows the university to get a better snapshot of COVID-19 prevalence among those showing no signs, but without the expense of diagnostic testing for every single person.

After reading about the SalivaDirect testing method from Yale, along with a similar method from University of Illinois at Urbana-Champaign, Berglund and his team were inspired to build a modified version of those two protocols that was optimal for their lab setting.

Surveillance refers to collecting data and producing information to identify the extent of a health threat like COVID-19, and then using those insights to develop an effective public health response. This is different from diagnostic testing (which Wyllie’s team developed) that can confirm whether an individual has the specific health condition.

Berglund emphasizes that pooled testing is not diagnostic. Instead, it pinpoints asymptomatic people who might be positive for COVID-19. It does so by detecting RNA signs of the coronavirus in saliva samples from multiple small groups of participants. To that end, the RNA Institute, in partnership with the UAlbany School of Public Health, is in the process of building 25,000 test kits, with three saliva collection test tubes per kit. Many have already been distributed across campus as part of pooled testing.

All students studying, working or visiting at any UAlbany campus during the fall 2020 semester must participate in the pooled surveillance testing program, according to the university website. All faculty and staff present on any campus, for any reason, are strongly encouraged to do so.

Students might find these are the easiest tests they take all semester. Tests are done by random sampling, and students are notified that “today’s the day” by email. Using the small plastic test tubes in their kits, Berglund says, “The individual will spit or drool into that tube and then wipe it down with an alcohol wipe, put it in the bag and then deposit that sample into a collection site.”

Students can fill their test tubes at home or on campus, but they should be alone. “We don’t want people congregating to do tests together,” Berglund says. “They do it in their bathroom, on their own.” They can then wrap the tube in a small biohazard bag, slip that into their backpack and just drop it off on campus.

Once the institute collects all the samples, about 1,000 or more per day, the staff groups them into pools of four. “We just have four students, or four faculty and staff, in a pool,” Berglund says. “That way, you can test in a more cost-effective way.” The majority of the pools are presumed negative, he notes, with COVID-19 positivity rates now very low in New York state.

For students, faculty or staff members in a “presumed-positive” pool, where testing indicates likelihood that at least one participant is positive, all four individuals are strongly recommended for diagnostic testing and quarantine, Berglund says. “But these are asymptomatic individuals,” he notes. “So, normally, you wouldn’t be picking them up at all.”

As the COVID-19 pandemic continues, Berglund has been most surprised at how contagious the virus is and how quickly it spreads. “I find it just fascinating,” he says. “As a person, it’s a little scary. But as a scientist, understanding that is interesting.”

[Read: Leading a COVID-19 Battlefield at a Border Hospital ICU.]

The scientists describe the satisfaction of seeing their laboratory efforts become practical resources in the effort against COVID-19. “I’m doing research on a broader level that really translates to the population,” Wyllie says. “And I like that translation of it.”

As for Berglund, “I really enjoy helping people,” he says. “I like seeing how my science can have a direct impact.”

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