A study published in the journal The Lancet Microbe has shown that testing for the presence of a single immune system molecule on nasal swabs can help detect hidden viruses not identified in standard tests.
As seen during the COVID-19 pandemic, potentially dangerous new viruses can begin to spread through the population long before the global public health surveillance system can detect them. “Finding a dangerous new virus is like looking for a needle in a haystack,” said Ellen Foxman, associate professor at Yale University in the United States.
“We found a way to significantly reduce the size of the haystack,” said Foxman, lead author of the study.
As reported by PTI, public health officials typically look to a few sources to look for early warning signs of an emerging disease. They study emerging viruses in animals that can transmit infection to humans. However, it is difficult to determine which of the many new virus variants represents a real danger.
They also look for outbreaks of unexplained respiratory conditions, which is how SARS-CoV-2, the virus that causes COVID-19, was discovered in China in late 2019.
However, by the time an outbreak of a new virus occurs, it may be too late to contain its spread. Nasal swabs are usually taken from patients with suspected respiratory infections and are tested for specific signatures of 10 to 15 known viruses. Most of the tests come back negative.
However, as Foxman’s team has previously observed, in a few cases, swabs from those who tested negative for “usual suspect” viruses still showed signs of activating antiviral defenses, indicating the presence of a virus.
The telltale sign was a high level of a single antiviral protein made by the cells lining the nasal passages.
The team applied extensive genetic sequencing methods to old samples containing the protein and, in one sample, found an unexpected flu virus called influenza C. The researchers also used this same strategy of retesting old samples to track missed cases of COVID-19 during the first two weeks of March 2020. While cases of the virus had emerged in New York State around the same time, testing was only readily available from weeks later.
Overall, 359 nasopharyngeal samples were tested for viruses from January 23-29, 2017 and 651 samples were tested from March 3-14, 2020.
In 2017, 251 (70%) of 359 samples tested negative for ten viruses (rhinovirus, influenza A and B, parainfluenza 1–3, respiratory syncytial virus A and B, human metapneumovirus and adenovirus) on the PCR respiratory virus panel multiplex ( RVP ; figure 1 ; appendix p 9). The RVP-negative samples came from hospitalized and outpatient children and adults, with 134 (53%) showing respiratory symptoms and 84 (34%) having a history of chronic respiratory disease, according to the study.
Hundreds of nasal swab samples taken from patients at Yale-New Haven Hospital during that time had tested negative for standard signature viruses. When tested for the immune system biomarker, the vast majority of these samples showed no evidence of antiviral defense system activity.
However, a few showed antiviral defense system activity. Of these, the team found four cases of COVID-19 that had not been diagnosed at the time.
The results show that testing for an antiviral protein made by the body, even if tests for known respiratory viruses are negative, can help identify nasal swabs most likely to contain unexpected viruses.
Screening for the biomarker can allow researchers to narrow down the search for unexpected pathogens, making it possible to monitor unexpected viruses using swabs collected during routine patient care, the researchers said.
Samples that possess the biomarker can be analyzed using more complex genetic testing methods to identify unexpected or emerging pathogens circulating in the patient population and trigger a response from the healthcare community, they said. .
(With PTI entries)
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