Emerging viruses could be easily detected with a simple nasal swab

As the COVID-19 pandemic demonstrated, potentially harmful new viruses can spread throughout the population long before the systems for monitoring global public health can catch them.

However, Yale researchers have discovered that examining nasal swabs for the presence of a single immune system molecule can help identify stealthy viruses that are missed by conventional tests; they reported in the journal Lancet Microbe on January 1^st, 2023.

Finding a dangerous new virus is like searching for a needle in a haystack. We found a way to significantly reduce the size of the haystack.”

Ellen F Foxman, Study Senior Author and Associate Professor, Laboratory Medicine and Immunobiology, Yale University

Public health officials typically consult a small number of sources when searching for early disease warning signs. They research new animal viruses that have the potential to infect humans. However, it can be challenging to pick out which of the hundreds or thousands of new viral variants actually pose a threat.

Additionally, they look for outbreaks of unexplained respiratory diseases, which is how COVID-19’s causative virus, SARS-Cov-2, was found in China late in 2019.

But it might be too late to stop the spread of a novel virus by the time an outbreak happens.

For the new study, Foxman and her team went back to an observation they had made in their lab in 2017, which they believed might offer a fresh method for keeping an eye out for unforeseen pathogens. Patients with suspected respiratory infections frequently have nasal swabs taken, which are then tested to look for specific signatures of 10 to 15 known viruses.

Most tests yield negative results. The swabs of some individuals who tested negative for the “usual suspect” viruses, however, still showed signs that antiviral defenses were activated, indicating the presence of a virus, as Foxman’s team noticed in 2017.

A significant concentration of a single antiviral protein produced by the cells lining the nasal passages served as the warning sign.

Based on that discovery, the researchers applied thorough genetic sequencing techniques to old samples that contained the protein and discovered an unexpected influenza virus, known as influenza C, in one sample.

During the first two weeks of March 2020, the researchers employed the same method of retesting old samples to look for COVID-19 cases that had gone unnoticed. Although the virus had started to cause cases in New York State at about the same time, testing was not accessible until several weeks later.

Numerous nasal swab samples taken during that time from patients at Yale-New Haven Hospital had tested negative for common signature viruses.

The vast majority of those samples revealed no evidence of antiviral defense system activity when examined for immune system biomarkers. However, a few did, and the team discovered four COVID-19 cases among them that had previously gone undetected.

The results show that testing for an antiviral protein produced by the body can help identify which nasal swabs are more likely to contain unexpected viruses, even if tests for known respiratory viruses are negative.

Researchers might be able to focus their search for unexpected pathogens by screening for the biomarker, which makes it possible to conduct surveillance for unexpected viruses using swabs obtained during routine patient care.

To identify unexpected or emerging pathogens circulating in the patient population and to prompt a response from the medical community, samples found to contain the biomarker can be analyzed using more sophisticated genetic testing techniques.