Lukas Flippo

The pandemic’s early weeks, marked by empty streets and overwhelmed ICUs, illuminated a critical need for accurate and accessible COVID-19 testing. In April 2020, Anne Wyllie, a research scientist at the Yale School of Public Health, released “a potentially game-changing paper” — from there, the study’s saliva-based testing protocol SalivaDirect would go on to revive the NBA and send kids back to school.

Early on in the pandemic, nasopharyngeal (NP) swabs were the standard method available for SARS-CoV-2 detection. Yet, the swabs were uncomfortable for many people, particularly for the elderly and young children. To make matters worse, supply chain bottlenecks led to a gutted testing capacity. Wyllie — having done previous research on bacteria detection in people’s saliva — was inspired to pursue saliva-based COVID-19 testing as a less invasive, faster and cheaper alternative. 

SalivaDirect started as a preprint released on Apr. 22, 2020. Wyllie, the study’s lead author, had spent six weeks working with saliva samples from inpatients and healthcare workers at Yale New Haven Health. The inpatients had varying degrees of severe COVID-19 infection. From this group, a combination of self-collected saliva samples and clinician-administered NP samples were analyzed to carry out direct, side-by-side comparisons.

The study found that saliva was more sensitive to SARS-CoV-2 detection than specimens collected using nasopharyngeal swabs. The NP swabs would often result in false negatives, while also yielding contradictory results over extended periods of time. 

On top of saliva collection being minimally invasive compared to nasal swabs, the study opened the door for at-home testing — with the saliva method, people could spit into a cup and mail it or drop it off at a testing site, Wyllie explained. This had the potential to greatly increase the country’s testing capacity.

“Saliva testing solves many problems,” Sterling professor of immunobiology and molecular, cellular and developmental biology Akiko Iwasaki said. “Saliva requires no swabs or viral transport media, both of which are in short supply. It also does not require a trained medical professional. [Nasopharyngeal] swab collection requires training and PPE, and is not always reliable if the swabs are not collected properly.”

Another major benefit of saliva collection was that it minimized the risk faced by healthcare workers performing COVID-19 tests. According to Wyllie, many individuals undergoing NP collection would cough or sneeze due to having the collection stick up their nose, further exposing workers to the virus. Saliva-based testing was safer.

Despite all of the benefits presented, one clear limitation of this study was the sample size — the NBA was ready to change that.

After the pandemic suspended the 2019-2020 NBA season, a Yale SalivaDirect-NBA partnership facilitated the players’ safe return to competition. It was a win-win — saliva-based testing would be more convenient and comfortable for players, while the SalivaDirect team could use the data to verify the accuracy of the saliva-based test.

“It was clear that [the NBA] wanted to use saliva to test players and staff because people don’t want to get these nasal swabs every day,” Nathan Grubaugh, an assistant professor of epidemiology and a joint senior author on the initial preprint, said. “They saw how saliva could be used in a way to help increase testing capacity … they also have this population of people that cannot social distance or wear masks by the nature of their job. And so to keep them safe, they have to do very regular testing.”

This partnership allowed the test to be validated in an asymptomatic cohort, according to Wyllie. 

With successful data from this NBA study, the U.S. Food and Drug Administration (FDA) granted an Emergency Use Authorization for SalivaDirect in August 2020.

“This is a great transition point where now we’re truly starting to be operational,” Grubaugh said. “We can focus on these labs that are already partnering with public schools across the country and we really hope to be able to impact our community and our surrounding community in the same way.”

The EUA allowed Yale to approve other labs to use the SalivaDirect testing protocol for use. Within days, the Grubaugh Lab had already received “hundreds of” emails inquiring about authorization, noted lab member Annie Watkins MPH ’21. As of March 2022, 174 American labs had administered some variation of the test, testing over 4.4 million samples since this authorization. 

The Yale team called SalivaDirect an “open-source” model, charging no royalties for their technology and posting all required protocols and reagents online. Steph Tan SPH ’23 emphasized that SalivaDirect is not commercialized — the sole objective is to increase accessibility to COVID-19 testing, Tan said.

“SalivaDirect is the world’s worst business model,” Wyllie said. “We don’t want prices to be any higher than they need to be.” 

Two breakthroughs had significantly lowered the cost of each SalivaDirect test. Based on continued experience storing saliva, Wyllie realized that expensive buffers, once considered crucial to the procedure, were not required to maintain efficacy. This lowered the cost of the collection of saliva from $28 to a mere few cents. Furthermore, Wyllie said that she and Grubaugh had managed to remove the RNA extraction step entirely. This made the test cheaper and faster than other test types.

In November 2021, the FDA approved the use of SalivaDirect for pooled COVID-19 testing, further cutting costs. This authorization came months after the SalivaDirect team published a paper supporting the pooling of saliva samples for the expansion of SARS-CoV-2 testing capacity. Led by Watkins and Wyllie, their study compared different pool sizes of saliva samples and found that the pooled method could be more cost-effective for SARS-CoV-2 testing, despite a slight decrease in test sensitivity.

“The main reason why we’re interested in this research is to get kids back to school,” Watkins said. “Pooling samples provides a more cost-effective option for screening so that schools can monitor students while bringing them back without too much of a financial burden.”

Although Yale was not among the schools considering SalivaDirect for routine testing — likely due to the costs and work involved in “completely changing the system over again,” Wyllie said — the protocol has aided many schools in bouncing back to in-person learning. 15 school districts have used SalivaDirect through the COVIDCheck Colorado program to test over 440,000 samples. Meanwhile, Ohio State University conducted nearly a million tests daily as of March 2022. 

SalivaDirect was also implemented in local testing clinics early this year. 

Sumaira Akbarzada MPH ’21 and her family came to the United States as Afghan refugees in the 1990s. Akbarzada, the community liaison for SalivaDirect, launched a new COVID-19 community testing program, “New Home, New Haven,” in early January. Through a partnership between SalivaDirect and New Haven-based nonprofit Integrated Refugee and Immigrant Services, this program offers free weekly testing to Afghan evacuees, along with other refugees and immigrants. According to Akbarzada, a COVID-19 test can cost $100 in Afghanistan, where the average monthly income is $300.

Over the summer, the Yale Pathology lab — a lab analyzing SalivaDirect tests — had teamed up with Clifford Beers, a children’s mental health clinic, to provide weekly saliva-based COVID-19 screening for the First Calvary Church’s summer program.

On Jan. 19, the state government-funded New Haven Green and Long Wharf testing sites started administering SalivaDirect tests.

“SalivaDirect is a PCR testing procedure that is a faster, easier, cheaper and more user-friendly approach to COVID-19 screening and diagnosis,” Yale School of Public Health Dean Sten H. Vermund wrote in an email to the News. “We are so pleased to see it available to the New Haven community.”

However, to address disparity in COVID-19 testing in New Haven, Yale Child Study Center associate research scientist Amanda Dettmer said that Yale should offer free saliva-based testing and free PCR testing to the New Haven community. She offered the University of California, Davis as a model — the university was already providing free saliva-based testing to its broader community. 

“It’s still shocking to me how quickly and easily I can schedule a test for myself or my dependents, versus for my mother,” Dettmer said. “[And] both of these are infinitely easier than for my friends who live just a few blocks away but have no affiliation with Yale.”

According to professor of epidemiology Albert Ko, saliva-based testing will be especially important as communities adapt to living with COVID-19 due to it simplifying regular testing.

The first COVID-19 case in New Haven was identified on Mar. 14, 2020. 

KAYLA YUP
Kayla Yup covers Science & Social Justice and the Yale New Haven Health System for the SciTech desk. For the Arts desk, she is covering the Humanities. With an interest in the intersections of the humanities and STEM, she is majoring in Molecular, Cellular & Developmental Biology and History of Science, Medicine & Public Health as a Global Health Scholar.