Surprisingly Old Viruses Retired Inside Bird Cells

Genetic fragments buried in the cells of songbirds indicate that a family of hepatitis-B-like viruses is at least 19 million years old, much more ancient than previously thought.

As much as 75 percent of the virus fragments, which are now harmless parts of the birds' genome, are identical to currently circulating viruses.

Viruses trick a cell into replicating their genetic codes to create more viruses, and some even insert themselves into the host's genome. (About 8 percent of the human genome is estimated to have come from invading retroviruses – viruses composed of genetic material called RNA.)

Sometimes viruses even pop themselves into the genetic material passed on to their host's offspring, and hence the virus — usually a functionless insertion in the genetic code at this point — passes from generation to generation.

So even as these viruses morph in the outside world, their ancient remnants are preserved in their host's genome. One way to reconstruct a virus' past is to look at viral gene sequences "fossilized" at different evolutionary time points in a host's genome.

In the new study, Clément Gilbert, a postdoctoral researcher, and Cédric Feschotte, both of the University of Texas at Arlington, looked at the avian hosts of viruses in the hepadnavirus family, which includes the modern hepatitis B virus. The virus family infects several bird and mammal species and is responsible every year for 600,000 human deaths from liver disease linked to hepatitis B, according to the World Health Organization.

The team found 15 fragments from the hepadnavirus family in the genome of a small Australian bird, the zebra finch, according to Gilbert.

They also found similar fragments in the genome of the dark-eyed junco, a common North American finch.

These two species diverged from each other an estimated 25 million years ago, indicating that the virus had infected one of their common ancestors, which passed the viral DNA down to both species.

Because the determination of divergence times is not always reliable, the researchers also looked at the differences between the fragments to determine how long ago they were identical. This resulted in a conservative age estimate of 19 million years, Gilbert told LiveScience. 

This work brought other surprises.

"When we compare our … fossil to the currently circulating viruses, we infer mutation rates that are extremely slow, like 1,000 times slower than what people used to think," Gilbert said, adding that it is not clear why short-term mutation rates would be so different from long-term ones.

As much as 75 percent of the ancient virus fragments were identical to currently circulating viruses. However, the contemporary viruses — sisters to the ancient ones — had been estimated to be less than 6,000 years old, he said. So the results suggest the origin of all avian hepadnaviruses (current and extinct lineages) is much deeper than the origin of the current viruses.

Prior to this study, no one had identified a hepadnavirus that had integrated into its host's genome and passed from generation to generation, according to Gilbert.

Wynne Parry
Wynne was a reporter at The Stamford Advocate. She has interned at Discover magazine and has freelanced for The New York Times and Scientific American's web site. She has a masters in journalism from Columbia University and a bachelor's degree in biology from the University of Utah.