The virus, named crAssphage, infects one of the most common gut bacterial species, Bacteroides. This bacterium is believed to be linked to obesity, diabetes and other gut-related diseases, researchers said.
Robert A Edwards, a bioinformatics professor at San Diego State University, working with visiting researcher and corresponding author on the study Bas E Dutilh, now at Radboud University Medical Center in The Netherlands, discovered the virus by accident.
They were using results from previous studies on gut-inhabiting viruses to screen for new viruses.
In the DNA fecal samples from 12 different individuals, they noticed a particular cluster of viral DNA, about 97,000 base pairs long, that the samples all had in common.
When Edwards and his colleagues checked this discovery against a comprehensive listing of known viruses, they came up empty.
The researchers then screened for the virus across the database of the US National Institute of Health's Human Microbiome Project (HMP), and Argonne National Laboratory's MG-RAST database, and again found it in abundance in samples derived from human feces.
To prove that the viral DNA they discovered in their computer data actually exists in nature, fellow SDSU virologist John Mokili used a technique known as DNA amplification to locate the virus in the original samples used to build NIH's database.
This was a new virus that about half the sampled people had in their bodies that nobody knew about.
"It's not unusual to go looking for a novel virus and find one. 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," Edwards said.
The fact that it's so widespread indicates that it probably isn't a particularly young virus, either.
"We've basically found it in every population we've looked at. As far as we can tell, it's as old as humans are," Edwards said.
Some of the proteins in crAssphage's DNA are similar to those found in other well-described viruses. That allowed Edwards' team to determine that their novel virus is one known as a bacteriophage, which infects and replicates inside bacteria.
They used innovative bioinformatic techniques to predict that this particular bacteriophage proliferates by infecting a common phylum of gut bacteria known as Bacteriodetes.
The research is published in the journal Nature Communications.