People with coronavirus infection with the Omicron variant often have significantly different viral levels in their nose, throat and saliva, and testing just one type of sample is likely to miss a significant proportion of the infection, according to two new papers that analyzed Omicron infections. Over time in a few people.
The papers, which have not yet been published in scientific journals, suggest that coronavirus tests that analyze both nose and throat swabs will pick up more omicron infections than those based on just a nasal swab. Although these combined tests are common in other countries, including Britain, none have been authorized in the United States.
“You can get a lot of bang for your buck if you use these mixed types of samples,” said Rustam. Ismagilov, a chemist at the California Institute of Technology and senior author of the two 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 domestic transmission of the coronavirus conducted in the Los Angeles area between November 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 a PCR test 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 that their infections began, allowing researchers to catch the first 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 the infection, allowing the scientists to make multiple comparisons between the amount of virus in different samples and in 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 detected in nasal swabs. “You can have very high, presumably infectious, viral loads in your throat or saliva before you take nasal swabs,” said Alexander Viloria Winnett, a graduate student at Caltech and author of the research paper.
(Other studies, including one by the Caltech team in late 2020 and early 2021, have found that coronavirus levels tend to be higher in saliva before the nose. “So, this advantage does not appear to be specific to Omicron, said Mr. Viloria Winnett. )
But later, when the viral load in the nose rose, it rose to levels higher, on average, than any of the oral samples, the researchers found.
Until then, there was a huge variance. For example, a woman had high levels of virus in her throat for the duration of her infection, while 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 consistently had higher viral loads in his nose than in his throat or saliva, even from the first days of his infection.
The data suggest that because of this difference, within the first four days of infection, “no single specimen type” will reliably infect more than 90 percent of infections, even with a highly sensitive PCR test.
Focusing on one sample type means “a really big part of the picture is missing,” said Reed Akana, a graduate student at the California Institute of Technology and author of the study.
Overall, the patterns in viral loads in nose and throat swabs were more different than for any other comparison of samples. The data suggest that whether subjects use PCR or antigen testing for the first four days of infection, testing these two sites at the same time will detect far more infections than either one alone.
In the second paper, the researchers evaluated the performance of the Quidel QuickVue At-Home antigen test, which uses a nasal swab, in a subgroup of 17 participants who enrolled in the study early in the course of their infection. All participants underwent daily antigen checks, as well as daily nasal, throat and saliva sampling.
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 percent of the time — a performance gap they attribute to the fact that the tests only measure virus in the nose, When people have high viral loads elsewhere.
The scientists said test manufacturers would need to make sure tests designed for the nose still worked in the throat; They warned that it is possible that some may not do so. But they urged companies and regulators to prioritize this research.
“If they could validate their current tests with a composite swab, we could catch a lot more infections than we do right now,” said study director Natasha Shelby, who is also an author on both papers.
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