Combination virus swabs would better detect Omicron, 2 papers suggest

People with Omicron variant coronavirus infections often have vastly different viral levels in their nose, throat and saliva, and testing just one type of sample risks missing a large proportion of infections, according to two new papers , who analyzed Omicron infections over time in a small number of people.

The papers, which have yet to be published in scientific journals, suggest that coronavirus tests that analyze both nasal and throat swabs would detect more Omicron infections than those that rely solely on a nasal swab. Although such combination tests are common in other countries, including Britain, none are yet authorized in the United States.

“You could get a lot more bang for your buck if you use these types of mixed specimens,” Rustem said. Ismagilov, a chemist at the California Institute of Technology and lead author of both papers. But in the United States, he said, “we’re stuck with no one 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, as Omicron was spreading rapidly. A total of 228 people from 56 households participated.

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

The first article focuses on 14 people who enrolled in the study before or at the same time their infections started, 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 scientists to make multiple comparisons between the amount of virus in different specimens and people at different times.

The researchers found significant differences in the viral load of different types of samples from the same individuals.

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

(Other studies, including one conducted by the Caltech team in late 2020 and early 2021, also found that coronavirus levels tend to increase in saliva before the nose. “So that feature at least doesn’t seem to be specific to Omicron,” said Mr. Viloria Winnett.)

But later, when the viral load peaked in the nose, it rose to higher levels, on average, than in either oral sample, the researchers found.

Even then, however, there was significant variability. For example, one woman had astronomical levels of virus in her throat throughout her infection, while viral levels in her nose repeatedly oscillated between detectable and undetectable over the course of more than a week. In contrast, another participant had consistently higher viral loads in his nose than in his throat or saliva, even from the first days of his infection.

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

Focusing on just one type of sample means “really missing a lot of the picture,” said Reid Akana, graduate student at Caltech and author of the study.

Overall, the patterns of viral loads in nasal and throat swabs were more dissimilar than any other sample comparison. Whether people use PCR or antigen tests, in the first four days of infection, testing both of these sites at the same time would detect far more infections than either alone, the data suggests.

In the second paper, 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 at the onset of their infections. All participants took daily antigen tests, in addition to providing daily nose, throat and saliva samples.

Researchers found that even when people had viral loads high enough to be considered infectious in at least one sample type, antigen tests were only positive 63% of the time – a performance gap they attribute to the fact that the tests only measure the virus in the nose, when people could have high viral loads elsewhere.

Test makers will need to ensure that tests designed for the nose still work in the throat, the scientists said; some may not, they warned. But they urged companies and regulators to prioritize this research.

“If they can validate their existing tests with a combined swab, we could catch so many more infections than we currently do,” said Natasha Shelby, the study administrator, who also authored both papers. .

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