Combined nasal, throat swab would better detect Omicron, say two papers

LOS ANGELES • People with coronavirus infections of the Omicron variant often have significantly different viral levels in their noses, throats and saliva, and testing just a single type of sample is likely to miss a large share of infections, according to two new papers, which analysed Omicron infections over time in a small number of people.

The papers, which have not yet been published in scientific journals, suggest that coronavirus tests that analyse nasal and throat swabs would pick up more Omicron infections than those that rely on just a nasal swab.

Although these combined tests are common in other countries, including Britain, none are yet authorised in the US.

"You could get a lot more bang for your buck if you use these mixed specimen types," said Dr Rustem Ismagilov, a chemist at the California Institute of Technology and senior author of both papers.

But in the United States, he said, "we are stuck with nobody doing it".

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

Every day for about two weeks, each participant collected nasal and throat swabs, as well as a saliva sample. The researchers performed polymerase chain reaction (PCR) tests and calculated the viral load in each specimen.

The first paper focused on 14 people who enrolled in the study before or at the same time that their infections began, allowing the 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 between the amount of virus in different specimens and people at different times.

Researchers found significant differences in the viral load of different sample types from the same individuals.

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

Other studies, including one conducted by the Caltech team in late 2020 and early last year, have also found that coronavirus levels tend to rise in saliva before the nose.

"So, that feature at least doesn't seem to be specific to Omicron," Mr Winnett said.

But later, when the viral load did spike in the nose, it rose to higher levels, on average, than in either of the oral samples, researchers found. Even then, however, there was significant variability. For instance, one woman had sky-high levels of virus in her throat throughout her infection, while the viral levels in her nose repeatedly flipped 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 his nose than in his throat or saliva, even from the earliest days of his infection.

Because of this variation, during the first four days of infection, "no single specimen type" will reliably catch more than 90 per cent of infections, even with a highly sensitive PCR test, the data suggests.

Test manufacturers will need to make sure that tests designed for the nose still work in the throat, the scientists said. It's possible that some may not, they cautioned. But they urged companies and regulators to prioritise this research.

"If they can validate their existing tests with a combination swab, we could be catching so many more infections than we are now," said Ms Natasha Shelby, the study administrator, who is also an author on both papers.

NYTIMES