New test aims to better detect viral infections

WASHINGTON (AP) — It happens too often: A doctor isn't sure what's causing someone's feverish illness but prescribes antibiotics just in case, drugs that don't work if a virus is the real culprit.

Now Duke University researchers are developing a blood test to more easily tell when a respiratory illness is due to a virus and not a bacterial infection, hoping to cut the dangerous overuse of antibiotics and speed the right diagnosis.

It works by taking a fingerprint of your immune system — how its genes are revving up to fight the bug. That's very different from how infections are diagnosed today. And if the experimental test pans out, it also promises to help doctors track brand-new threats, like the next flu pandemic or that mysterious MERS virus that has erupted in the Middle East.

That viral "signature could be quite powerful, and may be a game-changer," said Dr. Geoffrey Ginsburg, Duke's genomic medicine chief. He leads the team that on Wednesday reported that a study involving 102 people provided early evidence that the test can work.

Today, when symptoms alone aren't enough for diagnosis, a doctor's suspicion guides what tests are performed — tests that work by hunting for evidence of a specific pathogen. Fever and cough? If it's flu season, you might be tested for the flu virus. An awful sore throat? Chances are you'll get checked for strep bacteria. A negative test can leave the doctor wondering what germ to check for next, or whether to make a best guess.

Moreover, rapid in-the-office tests aren't always accurate and can miss infections. So patients may have blood or other samples sent to labs to try to grow any lurking bacteria and tell if it's to blame, additional testing that can take days.

"This is something we struggle with every day," said Dr. Octavio Ramilo, infectious disease chief at Nationwide Children's Hospital in Columbus, Ohio, who wasn't involved in the new study. Particularly with children, a respiratory virus and a bacterial infection "in the beginning look completely alike," he added.

Hence researchers at a number of universities are trying to harness a fairly recent discovery: As your immune system detects an invading bug, different genes are activated to fend off a viral infection than to fight a bacterial or fungal one. Those subtle molecular changes appear to be occurring even before you feel any symptoms. And they form distinct patterns of RNA and proteins, what's called a genomic fingerprint.

The Duke team discovered 30 genes that are switched on in different ways during a viral attack. The test essentially is a freeze-frame to show "what those genes are doing at the moment in time that it's captured," explained Duke lead researcher Dr. Aimee Zaas, an infectious disease specialist.

Small studies spotted that viral signature in people who volunteered to be infected with different influenza strains for science.

For a more real-world simulation, the researchers then analyzed blood samples stored from feverish people who had come to the emergency room — and who were eventually diagnosed, the old-fashioned way, with either some type of virus or a bacterial infection.

The genomic test proved 89 percent accurate in sorting out who had a virus, and did even better at ruling out those who didn't, Zaas reported Wednesday in the journal Science Translational Medicine.

It took 12 hours to get results. The researchers hope to speed that up so that it might work as quickly as some in-office tests.

Still, "it's a promising tool," said Ramilo, an Ohio State University professor who is doing similar research. He called the Duke study an important step toward creating a commercial test, and predicts one might reach the market within five years.

Why would a doctor want to know merely that a virus is present and not which virus? That's enough information to rule out antibiotics, Zaas said. Unnecessary antibiotic use is one factor in the growing problem of drug-resistant germs, which the government blames for more than 23,000 deaths a year.

Plus, if a dangerous new virus begins spreading, like MERS, this approach could help avoid quarantining people unnecessarily by telling right away which ones are virus-free, Ginsburg added.

In Ohio, Ramilo is exploring a more immediate need: When young infants have high fevers, they're often hospitalized while doctors run a battery of tests to find the fraction who have a serious bacterial infection. He is leading a study involving 22 pediatric emergency rooms to see if a genomic fingerprint approach could separate which babies really need all that testing.

But the virus-or-not question is just the beginning, Ramilo said. His research suggests genomic fingerprints also can distinguish a flu strain from other common viruses. And the Duke team is analyzing a huge study of students living in dormitories, to see if the genomic test detected who was incubating the flu before their first sniffle — and thus might be useful in stemming outbreaks.

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New technology transforms research in viral biology

Sep. 11, 2013 — Researchers at The Mount Sinai Medical Center have developed an innovative system to test how a virus interacts with cells in the body -- to see, for example, what happens in lung cells when a deadly respiratory virus attacks them.

In the journal Cell Host & Microbe, investigators say such a technique will not only speed basic research into viral biology, it will also help scientists improve vaccine production, generate novel antiviral compounds, and advance the development of viruses that attack cancer cells.

"We have a powerful system in place today to investigate ways in which viruses interact with cells, which has yielded fundamental insights. But has significant limitations such as cost, difficulty of use, and the problem that the cells we have to use are not in any way physiologically relevant to the virus we want to study," said the senior investigator, Benjamin tenOever, PhD, Fishberg Professor in the Department of Medicine and Department of Microbiology at the Icahn School of Medicine at Mount Sinai.

"The new system that we developed is much less costly, can be transferrable from the study of one virus to another, and, best of all, allows us to use the real virus in the real environment it infects," Dr. tenOever said.

Both the old and new systems essentially do the same thing -- they test the effect of the virus on every one of the "host factors" in a cell. Given that genomes encode about 25,000 different genes, each of which produces a different protein or molecule, researchers test what happens to viral growth and replication when each of those 25,000 factors are silenced. "By systematically silencing every one of those host cell factors, we can theoretically pinpoint a single protein that allows a virus to grow quickly, or another one that stops viral infection," Dr. tenOever said.

The technique in use today employs small interfering RNA (siRNA) molecules to silence the expression of genes in the host cell -- a robotic arm introduces a distinctive siRNA to small populations of human or animal cells.

But the system requires cells that are easy to grow as a substitute for natural cells. Immortal cancer cells or fibroblasts (connective cells) are often used, "which are not relevant in any way to the cells that most viruses attack. In order to study viruses this way, researchers have to modify them so that they can grow in these cells. This doesn't represent an accurate disease model," Dr. tenOever said. "If you want to know how flu viruses cause disease, you really want to look in the lungs or lung tissue of mammals -- which has not been possible in this kind of screen."

To make that possible, the researchers gave viruses the capacity to make those siRNAs -- eliminating the need for robots to administer individual siRNAs to individual host cells. "We created a virus family identical in all respects, except that each member of the family carries a different siRNA," Dr. tenOever says. "So in this swarm of viral soldiers, each one has a very small trick up its sleeve -- it can silence one thing in the host cell. And because of this, we can use the cells that viruses actually infect -- such as lung cells."

The researchers modified an alphavirus -- a class of viruses that includes a microbe that produces encephalitisso that 10,000 family "members" each carried a distinct siRNA -- which acts as a barcode of sorts. Then they allowed the virus to infect mice by mimicking the natural route of infection, such as a mosquito bite, and "let nature do its work," Dr. tenOever said. "We let evolution select for those viruses whose individual capacity to eliminate one thing gives them the growth advantage to outgrow their brothers and sisters." A week after the modified virus infection, researchers were able to "see" which virus grew faster than others, and could read the barcode that indicated which gene was silenced. They could also pinpoint the viruses that quickly died in cells. Such findings not only help researchers understand how the virus operates within the cell it infects, but also reveal excellent host targets for which to design antiviral drugs.

Once the virus family is generated for study, it can be amplified, so there is no need to re-engineer the virus library again, he added.

This screening system will likely have many clinical care applications, Dr. tenOever said. "It could be used to generate cell cultures that allow enhanced vaccine production. You could improve the capacity of a therapeutic virus to get into a particular tissue, to kill tumor cells, or to chase after metastatic cancer cells," he said. "There is potentially no end to uses of this technology."

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