People with coronavirus infections of the Omicron variant often have significantly different viral levels in their nose, throat and saliva, and testing just a single type of sample is likely to miss a large portion of the infections, according to two new papers, which discuss Omicron infections. analyzed over time in a small number of people.
The articles, which have not yet been published in scientific journals, suggest that coronavirus tests that analyze both nose and throat swabs would pick up more Omicron infections than those that rely on a nasal swab alone. While these combined tests are common in other countries, including Great Britain, none have yet been authorized in the United States.
“You could get a lot more bang for your buck using these mixed strains,” said Rustem Ismagilov, a chemist at the California Institute of Technology and the senior 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 household coronavirus transmission survey conducted in the Los Angeles area between Nov. 23 and March 1, when Omicron spread rapidly. A total of 228 people from 56 households took part.
Every day for about two weeks, each participant collected nasal and throat swabs, as well as a saliva sample. The researchers performed PCR testing and calculated the viral load, or level, in each sample.
The first paper focuses on 14 people who took part in the study before or at the same time their infections started, 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.
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 it was detectable in nasal swabs. “You can have very high, presumably infectious, viral loads in throat or saliva before nasal swabs,” said Alexander Viloria Winnett, a graduate student at Caltech and an author of the paper.
(Other studies, including one conducted by the Caltech team in late 2020 and early 2021, have also shown that levels of coronavirus tend to rise in nasal saliva.” So at least that feature doesn’t seem to be specific. for Omicron,” said Mr. Viloria Winnett.)
But later, when the viral load in the nose peaked, it rose on average to higher levels than in any of the oral samples, the researchers found.
Even then, however, there was great variability. For example, one woman had skyrocketing levels of virus in her throat during her infection, while viral levels in her nose repeatedly switched 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, “no specimen type” will reliably capture more than 90 percent of infections during the first four days of infection, even with a highly sensitive PCR test, the data suggests.
Focusing on a single sample type means “really missing a lot of the picture,” said Reid Akana, a graduate student at Caltech and an author of the study.
In general, the viral load patterns in the nasal and throat swabs were more different than in any other sample comparison. Whether people use PCR or antigen testing, during the first four days of infection, testing both sites at the same time would detect significantly more infections than either one alone, the data suggests.
In the second paper, the researchers assessed the performance of the Quidel QuickVue At-Home antigen test, which uses a nasal swab, in a subset of 17 participants who entered the study early in the course of their infections. All participants took daily antigen tests, in addition to providing daily nose, throat and saliva samples.
The researchers found that even when people had a viral load high enough to be considered infectious in at least one type of sample, the antigen tests were positive only 63 percent of the time — a performance gap they attribute to the fact that the tests only measure the virus in the nose, when people elsewhere may have a high viral load.
Test manufacturers will have to ensure that tests designed for the nose still work in the throat, the scientists said; it’s possible some won’t, they warned. But they urged companies and regulators to prioritize this investigation.
“If they can validate their existing tests with a combination smear, we could get so many more infections than we do now,” said Natasha Shelby, the study administrator, who is also an author of both papers.