COVID-19 Diagnostics: How Do Saliva Tests Compare to Swabs?

COVID-19 Diagnostics: How Do Saliva Tests Compare to Swabs?

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Since the early days of the pandemic, clinicians and researchers have been looking for alternatives to nasopharyngeal swabs. While samples collected from swabs are considered the gold standard in terms of generating accurate results, these tests require more supplies, place health care workers in closer contact with potentially infected individuals, and are difficult to scale up for mass testing. Saliva has been put forth as a low-cost, easy alternative, but it’s efficacy and accuracy remain points of contention.                                                      

Even as large universities have begun rolling out ambitious, saliva-based initiatives on campuses across the United States, private companies looking to develop rapid, in-home diagnostic tests have moved away from such tools. Trials of saliva-based testing being deployed in the field have yielded mixed results, and it remains unknown under what conditions saliva is most useful or how best it can be rolled into the existing testing framework.

We went into the jungle, into villages in the middle of the forest, and in very poor neighborhoods with mobile teams.

—Mathieu Nacher, Université de Guyane

Anne Wyllie, an epidemiologist at the Yale School of Public Health, has studied the use of saliva as a source of genetic material for the last decade, and more recently has investigated saliva’s role in testing for COVID-19. Wyllie has been tracking the emergent literature during the pandemic to see how often saliva outperforms nasopharyngeal swabs. Across the almost 30 studies she has analyzed, “it’s almost half and half,” she says.

To test the efficacy of saliva herself, Wyllie and 50 colleagues did their own side-by-side comparison and recently authored a commentary in the New England Journal of Medicine in which they reported the findings.

Among 70 patients admitted to Yale-New Haven Hospital with suspected cases of COVID-19, saliva samples often contained more copies of SARS-CoV-2 than did swab samples, and a higher percentage of saliva samples were positive up to 10 days after the initial diagnosis. And when applied to 495 health care workers, saliva tests identified two more asymptomatic cases than swabs did, leading the team to conclude in their letter, “our findings provide support for the potential of saliva specimens in the diagnosis of SARS-CoV-2 infection.”

In controlled health care settings, at least, it seems that saliva can perform comparably to nasopharyngeal swabs. But COVID-19 is a global pandemic, and many of the hardest-hit communities are rural, poor, or otherwise underserved. And those conditions may influence just how well saliva-based tests work.

A head-to-head comparison in the jungle

French Guiana—a territory along the east coast of South America—has been heavily affected by COVID-19, with confirmed infections in more than 3 percent of the region’s roughly 300,000 residents. Through boat travel, the virus has radiated along a convoluted network of rivers to infect remote villages in the Amazon rainforest. 

Mathieu Nacher, an epidemiologist at the Université de Guyane in French Guiana, tells The Scientist that he was approached by the French government about conducting clinical trials, including a comparison between swabs and saliva, just after the outbreak’s peak in early July.

Between July 27 and September 10, mobile field teams collected paired samples from 776 people across French Guiana, traveling “into the jungle, into villages in the middle of the forest, and in very poor neighborhoods” to recruit participants, Nacher says.

By bringing the testing directly into the field, researchers could assess the efficacy of these screening tools in real-world scenarios. “This is where you can really see their utility,” Wyllie tells The Scientist. Her work has shown SARS-CoV-2 remains stable within saliva for long periods of time, even at room temperature—a characteristic that comes in handy in sampling situations when temperature regulation may come at a premium, or not at all. 

After being collected, samples were kept cool and transported to the hospital in the capital of Cayenne for processing within 24 hours. Both samples underwent the same extraction protocols and PCR test to screen for the presence of three viral genes, N, E, and RdRP.