Researchers have known for some time that mammalian genomes contain DNA copies of retroviral sequences, known as endogenous retroviruses (ERVs). These sequences are passed down through generation after generation&mdash 8% of the human genome is known to consist of these retroviral elements. Their presence is somewhat logical, since an important step in retroviral replication is making a DNA copy of the virus’ RNA genome. But it seems that our genomes might have even more viral baggage than previously thought possible.

Earlier this year, researchers found the first instances of non-retroviral RNA virus sequences integrated into a mammalian genome. Now, a new paper in PLoS Pathogens takes a more expansive look at the phenomenon. Scientists examined over 5,000 genes from all known single-stranded RNA viruses that are not retroviruses and compared these to the genomes of 48 vertebrate species, including humans. They found sequences from RNA viruses in the Filovirus (Marburgvirus and Ebolavirus), and Bornavirus families in about half of these animals.

An obvious question is raised here: how did the sequences end up in the animal genome? Since these are not retroviruses, they don’t make DNA copies of themselves in order to reproduce. One plausible explanation is that host cells might have accidentally used a reverse transcriptase, such as telomerase, to generate DNA copies of the RNA viruses’ genomes at some point.

And why keep these sequences around anyways? Conserving these viral sequences may confer some immunity to the host, protecting it from future outbreaks, the authors speculate, though this connection has yet to be experimentally verified.

“It’s an interesting but unproven view that it’s there for a purpose. Those pieces of DNA could be expressed as a protein, offering some kind of early immune protection,” says Vincent Racaniello, a professor of microbiology and immunology at Columbia University.

Another important consequence of this discovery is that it turns out many viruses may be much older than previously thought. Without a fossil record to go off of, researchers had estimated that most known RNA virus types arose only about 50,000 years ago. They arrived at this age by using the known rate of mutation to calculate how far back you would have to go in time before the virus became unrecognizable. But this most recent discovery found a number of known viral sequences that were acquired at least 40 million years ago. Since this differs by a significant order of magnitude, scientists may have to reevaluate their method for estimating viral ages.

“It’s a bit of a conundrum, the molecular clock issue,” Racaniello says. “The rate of mutation itself hasn’t changed, but how you use it [to date a virus] is changing.”

Image of Marburg virus via Wikimedia Commons

And if you’d like to hear more about endogenous retroviruses, Vincent Racaniello’s ‘This Week in Virology’ podcast has an entire episode devoted to them.