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Do Not Sniff at Mucus Proteomics, or You Will Blow Chance to Confirm Viral Infection

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    A runny nose is a runny nose is a runny nose—always something indeterminate. It could indicate a cold, or maybe a bacterial infection. But which? Your Kleenex won’t tell you. And in ordinary circumstances, a doctor won’t either. So, you might be tempted to ask for an antibiotic, even though the drug would be useless against a viral infection—worse than useless, really, since unnecessary antibiotic use contributes to the problem of antibiotic resistance.


    But what if a runny nose was more telling than we knew? What if a nasal discharge was not just a slimy mess, but diagnostic gold? These questions were taken up by a team of scientists at Duke University Medical Center. They found that the identities and the abundances of certain proteins in mucus can determine whether a runny nose is due to a viral infection.

    Details of this work appeared February 21 in the journal EBioMedicine, in an article entitled “Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection.” This article describes how the Duke scientists used a human viral challenge model to discover and independently validate nasal proteins that can classify human influenza A and human rhinovirus infection from uninfected individuals.


    Specifically, the scientists sought to characterize this response through proteomic analysis of nasopharyngeal lavage in human subjects experimentally challenged with influenza A/H3N2 or human rhinovirus, and to develop targeted assays measuring peptides involved in this host response allowing classification of acute respiratory virus infection.


    “Unbiased proteomic discovery analysis identified 3285 peptides corresponding to 438 unique proteins, and revealed that infection with H3N2 induces significant alterations in protein expression,” reported the article’s authors. “These include proteins involved in acute inflammatory response, innate immune response, and the complement cascade.”

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    Ultimately, the Duke scientists identified a group of proteins that, when detected in specific quantities in the mucus, are 86% accurate in confirming the infection is from a cold or flu virus. The researchers hope their initial work identifying the protein signature could aid the development of a quick, noninvasive doctor’s office test to determine the cause of upper respiratory illness and appropriate treatment.


    “Every day, people are taking time off from work, going to emergency rooms, urgent care, or their primary care doctors with symptoms of an upper respiratory infection,” said Geoffrey S. Ginsburg, M.D., Ph.D., a senior author of the paper and director of the Duke Center for Applied Genomics & Precision Medicine (DCAGPM), which led the study. “Looking for these proteins could be a relatively easy and inexpensive way of learning if a person has a viral infection, and if not, whether the use of antibiotics is appropriate.”


    Although upper respiratory infections are among the most common reasons people visit the doctor in the U.S., healthcare providers lack tools to distinguish between a bacterial infection that might warrant antibiotics and a viral infection that would instead call for symptom relief.


    Widespread use of antibiotics for upper respiratory infections doesn’t benefit patients with viral illness and can contribute to antibiotic-resistant superbugs, Dr. Ginsburg noted. More precise diagnoses of these infections could be another tool to curb the development of superbugs, he said.


    For the trial, researchers infected 88 healthy adult volunteers with a common strain of cold or flu virus. Some participants didn’t get sick. Among those who developed infections, researchers found a distinct set of 25 proteins in fluid samples they gathered by flushing about two teaspoons of saline through the participant’s nasal passages.


    Duke researchers in genomics and precision medicine have spent the past decade exploring strategies for differentiating bacterial and viral infections with the goal of developing cost-effective diagnostic tools doctors could use in their offices.


    “In the past, science has focused on identifying the pathogen someone is infected with in the blood or other sample,” said lead author Thomas Burke, Ph.D., director of technology advancement and diagnostics at the DCAGPM. “Our approach flips the paradigm of how we look for infection. Instead of looking for the pathogen, we study the individual’s response to that pathogen and signature patterns in their genes, proteins, metabolites, and other biomarkers.”


    The Duke team has previously explored blood tests to examine a patient’s RNA for gene signatures to distinguish bacterial and viral infections in the upper respiratory tract and is working with a private company to develop potential diagnostics.


    Analyzing proteins in mucus is a less invasive approach and requires less processing than blood samples. The researchers hope additional studies verify the initial results and lead to the development of a paper-based test that could be used in doctor’s offices or even at home to determine whether a doctor’s visit is necessary, said Christopher Woods, M.D., a senior author and associate director of applied genomics at the DCAGPM.


    “The protein targets offer a faster, more cost-effective model for rapid screening and diagnoses of viral infections,” explained Dr. Woods. “If the data are verified, the model could be valuable in many circumstances, such as rural settings or developing countries with less convenient access to health care, or even as an airport screening tool during an outbreak of a particularly threatening strain of flu.”

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