As the Omicron virus spreads, some specialists advocate for the use of saliva-based testing, which can detect infections days before nose swabs can.
In the last two years, detecting COVID-19 infection has usually required a nose probe. Slender swabs have been injected deep into the recesses of Americans’ nasal passageways by health care personnel, while at-home test kits have required us to perfect the shallow double-nostril twirl.
However, the rapid spread of the Omicron strain, as well as concerns about the sensitivity of at-home tests, has reignited debate over whether sampling a different site, such as the mouth, is the best approach to detect the virus.
“The virus shows up first in your mouth and throat,” says Dr. Donald Milton, an expert on respiratory viruses at the University of Maryland. “That means that the approach we’re taking to testing has problems.”
According to some research, collecting saliva samples or swabbing the interior of the mouth can assist detect persons who are infected with the virus days before nasal swabs can.
The research is still developing, and the data paints a complicated picture, implying that saliva-based diagnostics have their own set of limitations. Many labs aren’t set up to process saliva, and none of the at-home antigen tests available in the US are approved for it.
Even the doubters of saliva admit that oral specimens have certain distinct advantages. With Omicron on the rise, some scientists believe that testing vendors, labs, and government officials should work faster to identify the optimum sample places and kinds for the virus.
In the early months of the pandemic, scientists began looking at saliva testing. They were keen to find a testing procedure that was more pleasant than the traditional deep nasopharyngeal swabs and didn’t require qualified health care workers or nose swabs, both of which were in low supply at the time. People might just spit into a tube and hand it over for processing using saliva.
Saliva testing has been questioned by some laboratory professionals as a viable approach to detect infection.
“There were concerns initially that saliva was not the gold standard sample, that it wasn’t the most sensitive sample,” says Glen Hansen of the clinical microbiology and molecular diagnostics laboratory at Hennepin County Medical Center in Minnesota.
However, by the fall of 2020, dozens of studies had concluded that saliva was a viable test sample.
“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 adds.
Saliva samples may be the best approach to detect infections early, according to evidence showing the virus appeared in saliva before it grew up in the nose.
Saliva samples had roughly three times as much virus as nose samples in the three days before symptoms appeared and were 12 times as likely to generate a positive P.C.R. result, according to Dr. Milton and his colleagues. According to the study, which has yet to be published in a scientific journal, more virus began to accumulate in the nose after that.
“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 adds.
The benefits of saliva may be more obvious with Omicron, which appears to replicate more quickly in the upper respiratory tract and has a shorter incubation period than previous types. Experts believe that any testing procedure that may consistently detect the virus sooner is very significant.
“I think Omicron has really changed the testing game because of how quickly the virus replicates and how quickly it spreads,” says Dr. Robby Sikka, who chairs the Covid-19 Sports and Society Working Group.
Omicron may also be stronger at replicating in the cells of the mouth and throat than other types, according to some specialists.
When it came to detecting the Delta variant, a group of South African researchers discovered that nose swabs functioned better than saliva swabs, but the opposite was true for Omicron. (Experts have yet to analyze the study, which used P.C.R. testing.)
More studies are required, and a modest new study conducted during an Omicron spike in San Francisco was less encouraging. Only two patients out of the 22 who tested positive on a fast antigen test using normal nose swabs were positive when their inner cheeks were swabbed. The researchers are currently investigating if throat swabs are more effective.
Saliva has its own set of trade-offs. While the virus appears to grow up in saliva early in the infection, the nose may be a better spot to detect it later on.
While the virus generally peaked first in saliva, it eventually rose to higher levels in the nose, according to researchers at the California Institute of Technology. Their findings show that very sensitive tests, such as P.C.R. tests, may be able to detect infections in saliva days before they are detected in nasal swabs, but less sensitive tests, such as antigen testing, may not.
According to some specialists, the facts on saliva is still mixed.
“There are these few studies that I have found really very interesting,” says Dr. Mary K. Hayden from Rush University Medical Center in Chicago.
However, Dr. Hayden cautioned that the new findings should be interpreted with caution because research has long demonstrated that nasopharyngeal tissues are the best for detecting respiratory viruses.
Some scientists are also concerned about practical issues. According to Joseph DeRisi, a biochemist at the University of California, San Francisco, who is also the president of the Chan Zuckerberg Biohub and an author of the cheek swab article, the mouth is “a little more of an uncontrolled environment compared to the nasal passages.”
“Did you drink a Coke right before you took the test? The pH will be different. And those things matter.”
Saliva can be “viscous and difficult to work with,” especially when patients are unwell and dehydrated, according to Dr. Marie-Louise Landry, director of the clinical virology laboratory at Yale New Haven Hospital.
In the end, multiple tactics may be required depending on the situation. Nasal swabs may be an excellent alternative for patients who have had symptoms for several days, while saliva may be best suited for large-scale surveillance screening of asymptomatic persons, according to Dr. Hansen.
“We need to get the right test into the right places,” he says.
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