Testing Tool that Accurately Distinguishes Between Viral and Bacterial Infection for Respiratory Illness Could Aid Fight Against COVID-19

A new testing tool that can quickly distinguish between viral and bacterial infections could help clinicians know when to correctly prescribe antibiotics and help in the fight against the COVID-19 pandemic.

In a study proving feasibility, researchers at Duke Health (Durham, NC, USA) showed that their testing technology can accurately distinguish between a viral and a bacterial infection for respiratory illness – a critical difference that determines whether antibiotics are warranted. And, importantly, the test provided results in under an hour. When patients complain of coughing, runny nose, sneezing and fever, doctors are often stumped because they have no fundamental tool to identify the source of the respiratory symptoms and guide appropriate treatments. The new tool can help resolve this issue.


The researchers have developed a gene expression method that diverges from current diagnostic strategies, which focus on identifying specific pathogens. The current tests are time-consuming and can only identify a pathogen if it’s specifically targeted by the test in the first place. Host gene expression, however, looks for a distinct immune signal that is unique to the type of infection the body is fighting. The immune system activates one set of genes when fighting bacterial infections and a different set of genes in response to a viral infection. After the team discovered these gene expression signatures for bacterial and viral infection, they developed this first-of-its kind test.

In a multisite study of more than 600 patients presenting to hospital emergency departments with respiratory infections, the tests identified bacterial infections with 80% accuracy and viral infections with nearly 87% accuracy. The current standard tests have about 69% accuracy. Tests provided results in less than an hour, and their accuracy was confirmed retrospectively using two different methods. Additional studies are underway to validate this approach in additional groups of patients. The researchers are also working to adapt the technology to produce more specific information, including whether the virus causing illness is influenza or SARS-CoV-2.

“Acute respiratory illness is the most common reason that people visit a health care provider when feeling sick,” said study lead Ephraim Tsalik, associate professor in the departments of Medicine and Molecular Genetics and Microbiology at Duke University School of Medicine. “Patients with these symptoms are inappropriately treated with antibiotics far too often due to challenges in discriminating the cause of illness, fueling antibiotic resistance. Our study shows that a rapid test to distinguish between these two sources of illness is possible and could improve clinical care.”

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