NEW YORK (GenomeWeb News) – A study appearing online last night in PLoS Biology suggests ancient viruses in the same family as hepatitis B found their way into bird genomes millions of years earlier than once thought.
By searching through some 200 vertebrate genomes, a pair of Texas researchers detected more than a dozen hepadnavirus-like fragments in the genome of the zebra finch — insertions that they subsequently tracked down in four more related bird species as well. Based on the types of insertions detected, they estimate that these viruses entered songbird genomes several times over the past 19 million or more years ago.
"We think that there's been insertions of at least 15 different viral particles," lead author Clément Gilbert, a post-doctoral researcher in Cédric Feschotte's genome biology lab at the University of Texas at Arlington, told GenomeWeb Daily News. "These different viral particles, most of them were coming from viral strains that were highly divergent from each other."
Bits of ancient viruses in present-day genomes can be used to learn more about viral history, Gilbert and Feschotte noted, explaining that "[g]enomic fossils closely related to modern viral groups are of particular interest as they have the potential to unveil otherwise inaccessible features of the long-term evolution of viruses."
For the current study, the duo focused on hepadnaviruses, a group of circular, double-stranded DNA viruses that includes hepatitis B. Although hepadnaviruses are DNA-based, they are not incorporated into the host genome as part of their replication process, Gilbert explained.
"We chose to look at hepadnaviruses first because we knew these were viruses that were replicating in the nucleus," he said, noting that hepadnaviruses that infect humans have been found in the liver cell genomes of chronically infected individuals.
As such, the team suspected that viruses in this family may also have the ability to become incorporated into some vertebrate host genomes in a more long-term way, integrating into germline cells and being passed on to subsequent generations, Gilbert explained.
To explore this possibility, he and Feschotte used TBLASTN to look for hepadnavirus sequences in all of the complete vertebrate genomes they could get their hands on.
Their search turned up 15 hepadnavirus sequence fragments in the genome of one vertebrate species: the zebra finch, Taeniopygia guttata.
These viral fragments seem to have originated from several different hepadnaviruses involved in numerous infection events, Gilbert noted. Overall, these sequences appear more similar to present day hepadnaviruses that infect birds such as cranes, geese, and ducks than they are to those infecting mammals, he explained.
When they used PCR experiments to specifically look for the same viral insertions in nuclear DNA from closely related birds that have not yet had their genomes sequenced, the researchers found hepadnavirus sequences in four more birds: the black throated finch, the scaly breasted munia, the gouldian finch, and the dark-eyed junco.
Because the viral sequences showed up in the same places as they had in the zebra finch genome, Gilbert noted, the researchers concluded that the viral fragments likely made their way into the genome prior to the divergence of the bird species from a shared common ancestor some 19 million or more years ago.
"[W]hereas we previously thought of hepadnavirus evolution on time scales of only a few thousand years, this paper shows that the true time-scale is in fact many million years," Pennsylvania State University biologist Eddie Holmes, who was not involved in the study, said in a statement. "Therefore, hepadnavirues, and likely many other viruses as well, are far older than we previously thought."
Although the insertions themselves appear to be non-functional and probably haven't had a strong impact on the birds' evolution, Gilbert explained, the fact that hepadnaviruses apparently infected these birds for such a long time suggests the viruses themselves may have influenced the course of the evolution in these species.
Finally, when the researchers compared the mutation rates in modern hepadnaviruses with those in ancient hepadnavirus sequences from bird genomes, they found that the long-term substitution rates are a fraction of those observed today — on the order of 1,000 times slower than rates predicted from present day hepadnaviruses.
Though the duo has come up with several hypotheses as to why this disparity in substitution rates exists, Gilbert noted that more research is needed to explore these theories.
To address such questions, they plan to continue scouring bird and other vertebrate genomes in hopes of finding both sequences from viral intermediates between ancient and modern hepadnaviruses. They also intend to look for remnants from additional virus families within vertebrate genomes.
"We are trying to find other examples like this for other viral families," Gilbert said. "And we hope that other people will put in efforts to screen these birds for the presence of circulating viruses, because that could provide us with an interesting model to study the replication and the infectious behavior of these viruses."