Newly Discovered Virus Lurking in Intestines

Is there a secret virus lurking in your gut? Probably.

A new study out of San Diego State University (SDSU) has found that more than half of people on earth have a newly discovered virus — dubbed crAssphage — that infects common gut bacteria known as Bacteroides. These bacteria are thought to be connected to obesity and diabetes. Learning more about the virus could shed light on those and other gut-related diseases.

Robert Edwards, a bioinformatics professor at SDSU, made the discovery with his colleagues by accident. He and Bas E. Dutilh, a professor who is now at Radboud University Medical Center in the Netherlands, were screening for new viruses by examining results from other studies.

When the pair looked at DNA in fecal samples from 12 people, they noticed that all of the samples contained a strange cluster of viral DNA. When they assembled the pieces and compared it to a list of known viruses, they came up empty.  (The cross-assembly software program they used, called crAss, was the inspiration for the virus' name.)

They also looked at databases from the National Institute of Health's Human Microbiome Project (HMP) and Argonne National Laboratory's MG-RAST database, but did not find the virus they had discovered.

That’s when John Mokili, a virologist from SDSU, used DNA amplification to grow many copies of the virus in order to prove that the DNA sequence Edwards and Dutilh had found actually came from a single living organism that exists in nature. Mokili identified the virus in the original samples that make up the NIH database.

"It's not unusual to go looking for a novel virus and find one," Edwards said in a press statement. "But it's very unusual to find one that so many people have in common. The fact that it's flown under the radar for so long is very strange." The research was published this week in Nature Communications.

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Because the virus is so widespread, it probably did not evolve recently. Edwards said they found crAssphage in every population they examined. 

"As far as we can tell, it's as old as humans are," Edwards said. 

Some of the proteins in it are similar to those found in other viruses. That’s what helped the researchers determine that crAssphage is a bacteriophage, an organism that infects bacteria and then replicates inside of them. CrAssphage thrives by infecting Bacteriodes, a common gut bacteria. CrAssphage could be involved in managing weight because of its effect on Bacteroides.

Bacteriodes live toward the end of the intestinal tract, and likely play a role in the link between gut bacteria and obesity. The researchers want to know where crAssphage fits in to that process. Edwards said the virus may mediate the activity of these Bacteriodes colonies. If researchers can isolate it, it could be used to help prevent obesity as well as other gut diseases.

"This could be a key to personalized phage medicine," Edwards said. "In individuals, we could isolate your particular strain of the virus, manipulate it to target harmful bacteria, then give it back to you."

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Dutilh said the finding is significant for a number of reasons.

“It highlights that the viral component of our gut flora is under-studied, similar between totally unrelated people, and evolves slower than previously thought,” he told Healthline.

The researchers do not yet know how the virus is transmitted. It is not found in infants, so it probably is not passed along from mothers to children.

What does the virus look like? The scientists think that crAssphage is circular, and more research indicates that it is a single organism, though it has been hard to isolate.

"We know it's there, but we can't capture it quite yet," Edwards said.

Dutilh said the team does not think the virus is harmful because it was found in many healthy people, though other known types of bacteriophages do cause disease.

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