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Sep 19, 2013

Genomic Test Distinguishes Viral from Bacterial Infections

  • Researchers at Duke Medicine report they have developed a blood test that showed more than 90% accuracy in distinguishing between viral and bacterial infections when tested in people with respiratory illnesses.

    According to those researchers, the test, which detects a specific genetic “signature” that the sick person's immune system expresses as a response to the virus, demonstrates a potential new method for diagnosing the source of illnesses that have long been tough to pinpoint. They published their study (“A Host-Based RT-PCR Gene Expression Signature to Identify Acute Respiratory Viral Infection”) in the September 18, 2013, issue of Science Translational Medicine.

    “We present evidence that targeted blood-based host gene expression patterns discovered with gene expression microarrays can be successfully transitioned to an existing in vitro diagnostic platform and used prospectively for classification of infectious respiratory diseases in cohorts that are representative of typical emergency department populations,” wrote the scientists.

    This is to say that the investigators believe the finding moves the technology closer to clinical use, where it could help patients get quicker diagnoses and treatments, while curbing the unnecessary use of antibiotics that don’t work on viral infections.

    “In instances such as pandemic flu or the coronavirus that has erupted in the Middle East, it’s extremely important to diagnose a viral illness far more accurately and speedier than can be done using traditional diagnostics,” said co-senior author Geoffrey S. Ginsburg, M.D., Ph.D., director of genomic medicine and professor of medicine at Duke University School of Medicine. “Current tests require knowledge of the pathogen to confirm infection because they are strain-specific. But our test could be used right away when a new, unknown pathogen emerges.”

    When infected by a virus, a person's immune system responds differently than when fighting a bacterial infection. These differences are evident at the genetic level, where certain genes are switched on during a viral attack, creating a fingerprint that broadly identifies the culpable pathogen.

    Unlike current tests that rely on evidence of the pathogen in the bloodstream–requiring knowledge of that particular bug to detect it–the new approach could be used to detect unknown emerging diseases, including potential bioterrorism threats.

    “This is important not only in viral pandemics where infection may be caused by unknown viruses but also in routine care where the decision to treat or not with antibiotics is paramount,” noted lead author Aimee K. Zaas, M.D., associate professor of infectious diseases and international health at Duke.

    The current study was a trial run of the blood test in a “real-world” setting. Among 102 people arriving at a hospital’s emergency department with fever, 28 had a viral infection, 39 had a bacterial infection, and 35 were healthy controls. Using the test, the Duke researchers were able to accurately classify more than 90% of the patients as having viral infections or not. The assay provided true positive identifications of viral infection in 89% of the cases, and correctly ruled out the negative cases 94% of the time.

    “We have established a ‘proof of concept’ that host expression of a relatively small set of genes, as measured by RT-PCR from blood RNA, can be used to classify viral respiratory illness in unselected individuals presenting at an emergency department for evaluation of fever,” summarized the Duke team in the journal article. “The development of this new assay and its validation in an independent real-world patient population is an important step on the translational pathway to establishing this platform for diagnostic testing.”



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