Certain families of single-stranded DNA virus are more than 40 to 50 million years old, according to investigators from the Institute for Advanced Study, Princeton, NJ, and the Fox Chase Cancer Center, Philadelphia. The investigators found remnants of circoviruses and parvoviruses in the genomes of diverse vertebrates from fishes to birds and mammals that had been integrated into their genomes at different times from the recent past to more than 50 million years ago. The research upends the conventional wisdom that most virus families are of very recent origin, and is published in the December Journal of Virology.
“Until recently, age estimates for all viruses except retroviruses were in the thousands of years, and nobody expected to be able to trace viruses beyond that time frame due to high mutation rates of the most commonly circulating viruses,” says Anna Marie Skalka of Fox Chase. “We showed that several families have been around for tens of millions of years, and have barely changed over that time frame.”
Viruses have long been speculated to be a source of novel animal genes, yet little evidence, except from retroviruses, has supported this idea. The team’s motivation included the desire to search for such evidence in other viruses.
“We first scanned all published vertebrate genomes for traces of single stranded RNA (ssRNA) viruses other than retroviruses,” says Skalka. The team then used a variety of techniques to devise a new method for determining the age of DNA sequences. “To our amazement, we discovered ancient fossils [viral sequences] in 19 vertebrate species that are related to certain currently circulating RNA viruses,” notably the deadly Ebolaviruses, and the Bornaviruses, she says. These results, published earlier this year, encouraged these investigators to look for ancient fossils derived from ssDNA viruses.
“Once again we were amazed to find sequences from replication (rep) and capsid genes from ancient viruses related to the Parvovirus and Circovirus families in 31 of the 49 vertebrate genomes we tested,” says Skalka.
While rep proteins from the circoviruses were already known—some of them selectively kill tumor cells—the relevant codes were certainly not known to have existed in vertebrates almost as far back as when the dinosaurs roamed earth. Skalka notes that there is no evidence yet that those coding sequences are expressed. “But should a beneficial role for these integrations be found, such as control of cancer progression, it may explain why these viruses were selected for over millions of years of vertebrate evolution.”
One additional notable finding is that the timeframe of the viral fossils’ appearance, 40-60 million years ago, was a time of rapid accumulation of exogenous and other elements into the genome, including multiple families of viruses, so-called “short interspersed elements” and pseudogenes. That’s a curious phenomenon which merits investigating, says first author Vladimir A. Belyi.
(V.A. Belyi, A J. Levine, A. Skalka. 2010. Sequences from Ancestral Single-Stranded DNA Viruses in Vertebrate Genomes: the Parvoviridae and Circoviridae Are More than 40 to 50 Million Years Old. Journal of Virology; 84.23: 12458-12462.)