As Omicron spreads, some experts are calling for a switch to saliva-based tests, which may detect infections days earlier than nasal swabs do.

By Emily Anthes

Over the past two years, diagnosing a coronavirus infection has often required probing the nose. Health care workers have inserted slender swabs deep into the recesses of Americans’ nasal passages, while at-home test kits have asked us to master the shallow double-nostril twirl.

“The traditional approach to diagnosing respiratory infections has been to go after the nose,” said Dr. Donald Milton, an expert on respiratory viruses at the University of Maryland.

But the rapid spread of the Omicron variant, and questions about the sensitivity of at-home tests, have rekindled a debate over whether the best way to detect the virus is to sample a different site: the mouth.

“The virus shows up first in your mouth and throat,” Dr. Milton said. “That means that the approach we’re taking to testing has problems.”

Collecting samples of saliva, or swabbing the inside of the mouth, could help identify people who are infected with the virus days earlier than nasal swabs do, some research suggests.

The science is still evolving, and the data paint a complex picture, suggesting that saliva-based tests have limitations of their own. Many labs are not currently set up to process saliva, nor are the at-home antigen tests available in the United States authorized for it.

But even the saliva skeptics acknowledge that oral specimens have some unique advantages. And with Omicron on the march, some experts say that testing companies, labs and federal officials should be working more urgently to determine the best sample sites and types for the virus.

“We need to be adaptable,” said Anne Wyllie, a microbiologist at the Yale School of Public Health, who is one of the developers of SalivaDirect, a noncommercial P.C.R. testing protocol. “I see so many either labs, or governments who are so fixated on a certain sample type or a certain test that even with changing data or test preferences, they don’t make the necessary adaptations to their testing programs.”

The case for saliva

Scientists began investigating saliva testing in the early months of the pandemic. They were eager to find a testing method that would be more comfortable than the deep nasopharyngeal swabs that were the standard at the time and that would not require trained health care workers or nasal swabs, both of which were in short supply. With saliva, people could simply spit into a tube and hand it over for processing.

Some laboratory professionals were skeptical that saliva testing would be a reliable way to detect infection.

“There were concerns initially that saliva was not the gold standard sample, that it wasn’t the most sensitive sample,” said Glen Hansen of the clinical microbiology and molecular diagnostics laboratory at Hennepin County Medical Center in Minnesota.

But by the fall of 2020, dozens of studies had suggested that saliva was a suitable sample for testing.

“There’s been a growing body of evidence that at the very least, saliva performs well — it’s as good as, if not better, when it’s collected properly, when it’s processed properly,” Dr. Wyllie said.

Evidence also emerged that the virus tended to appear in saliva before it built up in the nose, suggesting that saliva samples might be the best way to detect infections early.

Dr. Milton and his colleagues recently found that in the three days before symptoms appear and the two days after, saliva samples contained about three times as much virus as nasal samples and were 12 times as likely to produce a positive P.C.R. result. After that, however, more virus began accumulating in the nose, according to the study, which has not yet been published in a scientific journal.

The Food and Drug Administration has now authorized numerous saliva-based P.C.R. tests, which have proven popular for screening students in schools.

“Saliva really has turned out to be a valuable specimen type, and one that has increasingly been advocated as a primary testing sample,” Dr. Hansen said.

Saliva’s advantages may be more pronounced with Omicron, which appears to replicate more quickly in the upper respiratory tract and have a shorter incubation period than earlier variants. Any testing method that can reliably detect the virus earlier is particularly valuable, experts said.

“I think Omicron has really changed the testing game because of how quickly the virus replicates and how quickly it spreads,” said Dr. Robby Sikka, who chairs the Covid-19 Sports and Society Working Group and who helped bring saliva testing to the N.B.A. in 2020. (Both Dr. Sikka and Dr. Wyllie serve as unpaid board members for SalivaDirect.)

Some experts have also theorized that Omicron may be better at replicating in the cells of the mouth and throat than other variants have been.

A team of South African researchers recently found that while nasal swabs performed better than saliva swabs when detecting the Delta variant, the opposite was true for Omicron. (The study, which used P.C.R. tests, has not yet been reviewed by experts.)

More research is needed, and another small new study, conducted at a San Francisco testing site during an Omicron surge, was less encouraging. Of the 22 people who tested positive on a rapid antigen test using standard nasal swabs, only two tested positive when their inner cheeks were swabbed. The scientists are currently studying whether throat swabs perform better.

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