The US Food and Drug Administration has given Emergency Use Authorization to a fifth saliva-based test for COVID-19. The low-cost and noninvasive procedure developed by the Yale School of Public Health requires minimal processing and retains much of the accuracy of traditional nasopharyngeal swabs.
The United States has struggled to implement consistent and widespread testing throughout the pandemic, making it difficult for public health officials to track the spread of the virus. In addition, the equipment and reagents needed to carry out PCR tests have frequently run low, from the swabs needed to collect the sample to the reagents that extract viral RNA.
In a recent paper, published August 4 on the preprint server medRxiv, a team led by Yale postdoc Chantal Vogels detailed the new tool called SalivaDirect. A team composed of many of the same researchers had previously shown that saliva could be collected in any sterile container and that the saliva remained largely stable even when warm, negating the need for special tubes or preservatives.
“This is a huge step forward to make testing more accessible,” Vogels said in a recent press release. “This started off as an idea in our lab soon after we found saliva to be a promising sample type of the detection of SARS-CoV-2, and now it has the potential to be used on a large scale to help protect public health.”
Traditional COVID-19 testing is a two-part process: once the sample is collected, the virus’s RNA must be extracted before it can be detected by sensitive, PCR-based methods. SalivaDirect removes the extraction step, replacing it “with something that’s really simple. You add an enzyme, you heat it up, so you lose the most expensive step and the most time consuming and the most skilled [steps],” Nathan Grubaugh, an epidemiologist at Yale and a coauthor on the study, tells NPR.
The new test, which still relies on PCR to convert viral RNA to DNA and then amplify sequences, can run approximately 90 samples in fewer than three hours, STAT reports, with the potential to scale much higher in larger labs with automation. While most tests, spit or otherwise, are analyzed using PCR-based methods, there are other promising alternatives, such as loop-mediated isothermal amplification (LAMP), that have also received Emergency Use Authorization for testing using nasopharyngeal swabs.
Yale is offering SalivaDirect’s protocol open source, meaning researchers worldwide can take and adapt the method for use in their own labs depending on what resources they have available. The authors say they engineered their protocol to be as adaptive as possible to different PCR kits already on the market.
“Providing this type of flexibility for processing saliva samples to test for COVID-19 infection is groundbreaking in terms of efficiency and avoiding shortages of crucial test components like reagents,” Food and Drug Administration (FDA) Commissioner Stephen Hahn says in a press release announcing the emergency use authorization.
This same flexibility and relatively streamlined protocol also make SalivaDirect a cheaper alternative to traditional PCR tests, the authors say. The total cost of the reagents needed for one test is roughly $5, meaning it could be offered to the public for much less, perhaps as little as $10.
“This could be one the first major game changers in fighting the pandemic,” Andy Slavitt, a former acting administrator of the Centers for Medicare and Medicaid Services, tweeted in response to the news. “Rarely am I this enthusiastic . . . [With] a $10 test, you can test every day or every couple days.”
When compared to nasopharyngeal swabs, the authors found a “high agreement” of greater than 94 percent in detecting true positives between the two methods. In his Twitter thread, Slavitt gave a more conservative estimate of 88 percent to 94 percent accuracy when comparing SalivaDirect against both swabs and other saliva tests.
Martin Burke, a chemist at the University of Illinois at Urbana-Champaign who developed a similar saliva test, tells NPR that even a test with only 88 percent sensitivity can be extremely useful if it is plentiful enough for the kind of mass, repeated testing being carried out at his university. “If you do that twice a week, you’re going to catch 99% of the people—98% of the people,” Burke says.
SalivaDirect has already been used voluntarily by several teams of professional basketball players. Coaches, staff, and players from both the NBA and the National Basketball Players Association began voluntarily using the test in June, and their participation was central in gaining FDA Emergency Use Authorization. Yale is now partnering with the sports agencies to study asymptomatic spread. “We’re hopeful that our contributions to this work will help to advance the research in the interest of broadly accessible and minimally invasive testing,” John DiFiori, the NBA’s director of sports medicine, tells USA Today.