The Lancet Microbe: A simple nasal swab can provide early warning of emerging viruses

As the COVID-19 pandemic has shown, potentially dangerous new viruses can begin to circulate
among populations before they are detected by global public health surveillance systems.

However, researchers at Yale University found that testing for the presence of a single immune system molecule on a nasal swab could help detect stealth viruses not found in standard tests, they reported
Jan.
3 in The Lancet Microbios.

"Finding a dangerous new virus is like finding a needle in a haystack," said
Ellen Foxman, the study's senior author and associate professor of laboratory medicine and immunobiology.
"We found a way to significantly reduce the size of
the outbreak.
"

Public health officials often look for warning signs
of emerging diseases from a number of sources.
They study emerging viruses in animals that can be transmitted to humans
.
But among hundreds or thousands of new variants of the virus, determining which one is the real danger is difficult
.
They look for outbreaks of unexplained respiratory diseases, which is why the SARS-Cov-2 virus that causes COVID-19 was discovered in China in late 2019
.

However, when a new virus breaks out, it may be too late
to contain its spread.

In the new study, Foxman and her team reviewed an observation made in the lab in 2017 that they thought could provide a new way
to monitor for accidental pathogens.
Nasal swabs are usually taken from patients with suspected respiratory infections and are used to detect specific features
of 10 to 15 known viruses.
Most test results were negative, but as Foxman's team observed in 2017, in a few cases, cotton swabs from people who tested negative for the "common suspect" virus still showed signs that antiviral defenses were activated, suggesting the presence of the
virus.
A clear sign is high levels of an antiviral protein produced by nasal channel cells
.

Based on this discovery, the researchers applied comprehensive genetic sequencing methods to older samples containing the protein and accidentally discovered a flu virus
called influenza type C in one of the samples.

The researchers also used the same strategy, retesting old samples for COVID-19 cases
missed in the first two weeks of March 2020.
While cases of the virus also appeared in New York State around the same time, testing was not available until weeks later
.
During this time, hundreds of nasal swab samples taken from patients at Yale-New Haven Hospital tested negative for the standard characteristic virus
.
When tested for immune system biomarkers, the vast majority of samples showed no signs
of activity against the viral defense system.
But a few did; Of these cases, the team found 4 cases
of COVID-19 that were not diagnosed at the time.

The findings suggest that even if tests negative for known respiratory viruses, tests on antiviral proteins produced by the body can help determine which nasal swabs are more likely to contain unexpected viruses
.

Specifically, screening biomarkers allows researchers to narrow their search for unexpected pathogens, making it possible
to monitor accidental viruses using cotton swabs collected during routine patient care.
Samples found to have biomarkers can be analyzed using more sophisticated genetic testing methods to identify unexpected or emerging pathogens circulating in patient populations and quickly initiate responses in the health care community
.

Nagarjuna R.
Cheemalla and Jason Bishai of Yale University are co-lead authors of the paper, along with former Yale researchers Amelia Hanron and Joseph R.
Fauver
.