Combined Covid swabs would better detect Omicron, 2 papers suggest

People with omicron variant coronavirus infections often have markedly different concentrations of virus in their nose, throat and saliva, and testing just a single type of sample is likely to miss a large proportion of infections, according to two new papers analyzing omicron infections in the over time in a small number of people.

The work, which has not yet been published in scientific journals, suggests that coronavirus tests that analyze both nasal and throat swabs would detect more omicron infections than those based only on a nasal swab. Although these combined tests are common in other countries, including the UK, none are yet approved in the United States.

“You could get a lot more bang for your buck using these mixed sample types,” Rustem said Ismagilov, a chemist at the California Institute of Technology and senior author of both articles. But in the United States, he said, “we’re stuck that no one is doing it.”

Both papers are based on data collected during a study of household coronavirus transmission conducted in the Los Angeles area between November 23 and March 1, when omicron was spreading rapidly. A total of 228 people from 56 households took part.

Each participant took nasal and throat swabs and a saliva sample daily for about two weeks. The researchers performed PCR tests and calculated the viral load, or level, in each sample.

The first paper focuses on 14 people who enrolled in the study before or at the same time as their infections began, allowing researchers to capture the earliest stage of infection.

This group of participants provided a total of 260 nasal swabs, 260 throat swabs and 260 saliva samples over the course of their infections, allowing the scientists to make multiple comparisons of virus levels in different samples and people at different times.

The researchers found significant differences in viral loads of different sample types from the same people.

In most participants, the virus was detectable in saliva or throat swabs before it was detectable in nasal swabs. “You can have very high, presumptively infectious, viral loads in your throat or saliva before nasal swabs,” said Alexander Viloria Winnett, a Caltech graduate student and author of the paper.

(Other studies, including one conducted by the Caltech team in late 2020 and early 2021, have also found that salivary coronavirus concentrations tend to increase in front of the nose. “So at least this trait doesn’t appear to be specific to Omicron, said Mr. Viloria Winnett.)

But later, when the viral load in the nose rose, it rose to higher levels on average than in any of the oral samples, the researchers found.

However, even then there were considerable fluctuations. For example, one woman had sky-high levels of virus in her throat during her infection, while virus levels in her nose repeatedly went back and forth between detectable and undetectable over the course of more than a week. On the other hand, another participant had consistently higher viral loads in the nose than in the throat or saliva in the first few days of his infection.

Because of this variation, “no single sample type” will reliably catch more than 90 percent of infections during the first four days of infection, even with a highly sensitive PCR test, the data suggest.

Focusing on a single sample type means “really missing a big part of the picture,” said Reid Akana, a Caltech graduate student and author of the study.

Overall, the patterns of viral loads in the nasal and throat swabs were more disparate than any other sample comparison. Regardless of whether people use PCR or antigen testing, testing these two sites simultaneously would detect significantly more infections than either one individually in the first four days of infection, the data suggest.

In the second study, researchers evaluated the performance of the Quidel QuickVue At-Home Antigen Test, which uses a nasal swab, in a subset of 17 participants who enrolled in the study early in the course of their infections. All participants underwent daily antigen testing in addition to providing daily nasal, throat, and saliva samples.

The researchers found that even when people had viral loads high enough to be considered infectious in at least one type of sample, the antigen tests were only positive 63 percent of the time — a performance gap they attribute to this that the tests only measure the virus in the nose when people elsewhere may have high viral loads.

Test makers need to ensure that tests designed for the nose also work in the throat, the scientists said. It’s possible some don’t, they warned. However, they urged companies and regulators to prioritize this research.

“If they can validate their existing tests with a combination swab, we could get so many more infections than we do now,” said Natasha Shelby, the study leader, who is also the author of both articles.

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