Saliva PCR tests may detect disease earlier in the course of an infection

After her children were exposed to COVID, Megan, a woman in Illinois, took them to get tested. A rapid test from the local drugstore might have sufficed, but her son Brennan really did not like the nasal swab—it tickled, it was sometimes painful, and it was just not a fun experience. So Megan took her children to a testing site where Brennan spat into a tube that was then sent off to a lab for processing. The results came back in less than 24 hours.

COVID testing has advanced rapidly since early in the pandemic, when people had to get deep “brain tickling” nasal swabs at a doctor’s office and wait days for results. The University of Illinois at Urbana Champaign (UIUC), Yale University, the Rockefeller University and others have now independently developed an array of saliva-based tests.* These tests are less invasive, can be processed faster and, in some cases, are more sensitive than nasal-based assays.

Whereas nasal swabs can be somewhat unwieldy for everyday use, “it’s fairly easy to provide a saliva sample repeatedly,” says Rebecca Lee Smith, an infectious disease epidemiologist at UIUC and a scientific advisor for the program that developed covidSHIELD, the saliva test Brennan took.

CovidSHIELD is a polymerase chain reaction (PCR) test, a highly sensitive molecular assay that involves amplifying genetic material from SARS-CoV-2, the virus that causes COVID, to a detectable level. PCR analysis is usually but not always done in a laboratory.

Once a covidSHIELD saliva sample reaches the laboratory, scientists drop it into a hot-water bath to kill any existing virus and neutralize saliva components that might interfere with the test. The sample is now ready to undergo amplification. “Primers,” short fragments of genetic material, are added to the sample. As Smith explains it, primers are “a little ‘idea’ of what the virus looks like in the RNA [genetic material].” The RNA from the virus is converted into complimentary DNA (cDNA). The primer tries to connect itself to cDNA from the virus and make a copy. As the process is repeated, or “cycled,” any cDNA is amplified through these copies until it can be easily identified and deemed a positive sample.

The covidSHIELD procedure is able to skip a traditional RNA extraction step. Instead it uses heat and chemical treatments to release the viral RNA. This enables the test’s developers to promise results in less than 24 hours. The average turnaround time for results is even faster, according to Beth Heller, a spokesperson for SHIELD Illinois, a nonprofit unit of the University of Illinois System that administers the test in the state. “We are, right now, averaging 13 hours” from sample collection to results, she says.

The time lag between taking a COVID test and getting the result is a critical factor in evaluating any diagnostic. Along with overall testing sensitivity, it is part of a broader debate about the use of PCR versus rapid antigen tests. Antigen tests are mainly nasal-swab-based, although researchers are working on an accurate saliva-based version. And they work by testing for the presence of viral antigens—bits of the virus that provoke an immune response—using a specialized testing strip.

Proponents of antigen tests argue that their speed and low cost make them more suitable as a public health tool. “A PCR test, especially one that has to be sent out to the laboratory, should really be reserved for medicine,” such as when a doctor diagnoses a patient, says epidemiologist Michael Mina, who has advised President Joe Biden and his administration on testing and who is chief science officer of eMed, a company that sells antigen tests that are verified through a telehealth platform.

PCR tests’ extreme sensitivity is one of their main problems in a public health context. “I don’t want [someone] to have a positive test if [they are] not infectious anymore, because if they’re positive, I’m going to tell them to isolate for 10 days,” Mina says. “And if they’re not infectious anymore, me telling them to isolate for 10 days is bad public health.”

But Smith, who was part of a team whose research informed the U.S. Centers for Disease Control and Prevention’s policy on how to use antigen tests, says saliva-based PCR assays have very different use cases than those of antigen tests. “Saliva-based PCR tests are very sensitive, and they can actually pick up infections before you’re infectious,” Smith says. They are as sensitive or even more sensitive than nasal-swab PCR assays. This may be especially true with the Omicron variant because it replicates in the mouth and throat more than previous variants did.

So if given the option, which test do you take? The answer depends on your detection sensitivity needs. For example, symptoms can start much sooner in vaccinated individuals infected with Omicron than they did with previous variants because of the body’s built-up immune response before the virus has had time to replicate much. Antigen tests can continue to return a negative result until well into symptom onset, so a more sensitive test, such as a saliva-based PCR, could detect an infection earlier.

Saliva-based tests are good for answering questions such as “I think I was exposed this weekend. Am I infected? Am I going to be infectious tomorrow?” Smith says. By contrast, antigen tests are useful for determining if someone is actively contagious. “Rapid antigen tests are great for a quick check of ‘Hey, I have these symptoms. am I infectious right now?’” she says.

Once someone is no longer infectious, saliva PCRs may still show up as positive because of their sensitivity. At this point, an antigen test may be more appropriate for determining when someone is no longer infectious, Smith says. “I don’t recommend any PCR [test] for exiting isolation, but antigen tests can be very helpful in that regard,” she adds.

Earlier in the pandemic, saliva-based COVID tests required visiting a health care professional. But covidSHIELD and other recently developed saliva tests have made them more accessible. That accessibility is also starting to extend into the home: the U.S. Food and Drug Administration has already granted emergency use authorization for several self-collected, saliva-based PCR tests—including one using covidSHIELD technology. “Self-collected” means that saliva is collected without the presence of a trained observer. This removes the need to travel to a testing site and opens up the possibility of collecting samples at home—although they still must be shipped to a lab for analysis. SHIELD T3, a spinoff company owned by the University of Illinois System, recently started producing covidSHIELD self-collection kits that contain all the directions and materials needed to provide a sample and deliver it to a collection point for lab testing, according to the company’s CEO David Clark. SHIELD T3 is currently offering the kits on a limited basis to schools, colleges and some companies, Clark says. Ultimately, he and his team envision distributing the kits via vending machines or handing them out at workplaces, for example.

Looking to the future, the same saliva-based PCR technology could be used to identify other pathogens in addition to COVID, such as influenza or respiratory syncytial virus, according to Smith. “We are starting to get to work on a project for what’s called a multiplex PCR,” she says. “Rather than just testing for COVID-19, we would look for other respiratory pathogens that cause similar symptoms.”

*Editor’s Note: The author of this article is currently employed by the University of Illinois Extension, which is part of the University of Illinois at Urbana Champaign (UIUC). But he is not associated with the division of UIUC that developed the saliva test and has no financial interest or stake in it.

Anthony Warmack is a freelance journalist and science writer based in the Illinois valley.  His interests are in the intersection of society and science, public health, food systems, and experiential learning. Follow him on Twitter @AnthonyWarmack.

Rae Ellen Bichell and Kaiser Health News

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