Testing nose and throat would better detect omnin variant, researchers say

People with omicron-variant coronavirus infections can have significantly different viral loads in their nose, throat and saliva, and performing a single type of test is likely to miss many infections, according to two new research.

The articles, which have not yet been published in scientific journals, suggest that coronavirus tests that look at samples from the nose and throat would detect more omicron infections than those performed with just the nasal swab. While these combined tests are common in other countries, including Great Britain, none are authorized in the United States.

“You can get a lot more returns if you use these types of mixed samples,” said Rustem 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 nobody doing it.”

Both articles are based on data collected during a family transmission study of coronavirus conducted in the Los Angeles area between November 2021 and March of this year, when the omicron variant was spreading rapidly. 228 people from 56 households participated.

Daily for about two weeks, each participant collected nasal and throat swabs, as well as a saliva sample. The researchers performed PCR tests and calculated the viral load in each sample.

The first paper focuses on 14 people who enrolled in the study before or when their infections started, allowing the researchers to capture the early stage of the infection.

This group of participants provided a total of 260 nose 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 samples 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 appearing in nasal samples. “You can have very high viral loads, presumably infectious, in your throat or in your saliva before the nasal swabs,” said Alexander Viloria Winnett, a graduate student at Caltech and one of the authors of the paper.

Other studies, including one by the Caltech team in late 2020 and early 2021, also found that the viral load of coronavirus tends to increase in saliva before the nose. “So this feature, at least, doesn’t appear to be omicron-specific,” Winnett said.

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

Even so, there was significant variability. For example, one woman had sky-high levels of virus in her throat throughout her infection, while viral levels in her nose repeatedly ranged from detectable to undetectable for more than a week. On the other hand, another participant had, from the first days of infection, higher viral loads in the nose than in the throat or saliva.

Because of this variation, in the first four days of infection, no one type of sample will reliably detect about 90% of infections, 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 graduate student at Caltech and also an author of the study.

Overall, the patterns of viral loads from the nose and throat swabs were more different than any other sample comparison. Regardless of whether people were using PCR or antigen tests, in the first four days of infection, testing these two sites simultaneously would detect significantly more infections than either one alone, the researchers say.

In the second article, the group evaluated the performance of the Quidel QuickVue At-Home antigen test, the self-test, which uses the nasal swab, in 17 participants who enrolled in the study at the onset of their infections. All participants had daily antigen tests, in addition to providing daily nose, 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, antigen tests were positive only 63% of the time — a performance gap they attribute to the fact that that tests only measure the virus in the nose, when people may 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, but cautioned that some might not work. They urged companies and regulators to prioritize this research.

“If they can validate their existing tests with a combined swab, we could catch a lot more infections than we are now,” said Natasha Shelby, the study’s administrator, who is also an author of both papers.

Translated by Luiz Roberto M. Gonçalves