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Duke Researchers Say Gene Studies Can Help Diagnose Flu, Other Infectious Diseases

Duke University researchers have found a way to diagnose infectious diseases such as flu and staph infections more quickly by looking for responses in a patient’s genes.

Genomics, a field of genetics that takes into account the entire gene sequence, can identify diseases more quickly and accurately than typical methods, according to studies published earlier this month in PLOS ONE, a peer-reviewed online journal of science and medicine.

The researchers examined the ribonucleic acid, or RNA, from blood samples taken from patients. They found that the RNA profiles changed in specific ways among patients exposed to infectious viruses or bacteria, according to Geoffrey Ginsburg, director of genomic medicine at Duke’s Institute for Genome Sciences & Policy and an author on both studies.

“Other diagnostic approaches have to be very specific as to what they think the pathogens are,” Ginsburg said. “Our approach doesn’t care, because it takes advantage of the host response,”

To conduct their research, the scientists inoculated 41 people with H1N1 or H3N2 flu before analyzing their blood samples. Specific changes to the RNA profile, called the Influenza Factor, were found in patients exposed to either flu strain. The test was able to distinguish infected from non-infected individuals with 94 percent accuracy.

In a second study, the researchers found a similar factor for diagnosing staph, a common bacterial infection.

The genomic method can reveal an infection before symptoms appear, allowing treatment to begin almost immediately, Ginsburg said.

“If you have been exposed, we can make the prediction on whether you are going to get sick, and consider starting an antiviral medication,” Ginsburg said. “Such early intervention is likely to make the treatment more effective.”

Early treatment could give schools, hospitals and other places where illness spreads quickly a better chance of controlling an outbreak.

“Think back to the SARS epidemic [of 2002-2003], when entire schools were being closed and people were being quarantined because we didn’t know whether they were actually going to be infected and get sick,” Ginsburg said. “A cheap and rapid test would have offered a distinct advantage, from a public health point of view.”

The genomic response approach also could have been useful during the 2009 flu pandemic, which stemmed from a new strain of the virus, said Christopher W. Woods, associate professor of medicine, pathology and global health at Duke and lead author of the flu study.

“The original tests didn’t perform very well in detecting H1N1, because it was something new,” Woods said. “A test like ours would have responded and suggested influenza infection.”

In addition to halting or lessening the severity of an illness, antiviral medication will stop a virus from “shedding,” which is how it is spread from one person to another, the researcher said.

Yet another advantage would be the ability to rapidly distinguish between bacterial and viral infections, Woods said.

Antibiotics are not effective against viruses, but they are sometimes prescribed when the origin of an illness isn’t clear. Overuse of antibiotics causes resistant strains of bacteria to develop, posting a further threat to health, Woods said.

“It’s one of the major issues we are trying to address,” Ginsburg added. “Too many times people are treated for bacterial infections when they have a virus.”

Zach Moore, epidemiologist with the N.C. Division of Public Health, said flu testing is done currently with nasal or throat swabs, typically on patients who are already experiencing symptoms. Results from those tests are usually available within a few hours.

Some doctors use a rapid flu test that produces more immediate results, but those results are less reliable, Moore added.

“The work using genomes sounds interesting,” he said. “I’m looking forward to hearing more about it.”

Research leading to the discovery began in 2007 with $30 million in funding from the U.S. Department of Defense, Ginsburg said.

“The military is interested in maintaining the health of troops,” he said. “If a viral infection is running through a contingent in the field, it can put them in a compromising situation. With our rapid screening diagnostics, military leadership could know almost immediately if there’s a pathogen involved and take action against it.”

More work will be needed before genomic diagnoses can be put into routine use by doctors.

“If we were working with a commercial firm, it could be two or three years before we have something robust, reproducible and ready,” Ginsburg said. “If we were called upon to move fast and had resources from the military or government, it could be quicker – possibly in a few months.”

Eventually, blood tests that measure genomic response may be carried out at home, he said.

“I could imagine a scenario where this could be translated to a simple device, like a home pregnancy test, where you could test a drop of blood to see if you have been exposed,” Ginsburg said. “That would allow you to take action long before you find yourself at the doctor’s office feeling lousy.”

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