Virus DNA in Birds: A Surprising Number of Viral Sequences are Expressed

Like other organisms, the genomes of birds are riddled with DNA sequences from retroviruses. A study in mBio this week examined the genomes of three species of birds for these proviruses and followed the

Is it a chicken with viruses in it, or viruses with some chicken thrown in?

expression of genes during development. What role these viral proteins might play in bird biology is not yet known, but in chickens, a surprising 20% of proviruses are translated during embryo development.

Genomes are works in progress

All genomes are cobbled together works-in-progress. Scientists have long known that the human genome, for example, is not all human: like most every other genome studied to date, a good chunk of the DNA we call “human” is actually made up of proviruses, sequences that retroviruses have deposited there to take advantage of the cell’s ability to copy DNA and translate that DNA into working proteins. These proviruses can either be inherited in the DNA we get from our parents (they’re called “endogenous retroviruses”), or they can be picked up during our lifetime (called “exogenous retroviruses”).

Many proviruses in birds are translated during development

Bird genomes, too, contain proviruses, but the number and character of these viral sequences have not been studied in detail. The authors of the paper in mBio examined the genomes of the chicken, turkey, and zebra finch to learn more about the evolution of the viruses and of the birds themselves.

Stepher Goff of Columbia University edited the study for mBio. He says the numbers of proviruses the researchers found in bird genomes might surprise some people: the zebrafinch genome contained the most proviruses (1221), while the chicken (492) and turkey (150) carried fewer. “These are large numbers,” says Goff, “but they’re in accord with what we’ve seen in mammals.”

What’s more surprising, says Goff, is that many of these proviruses appear to be active. In chickens, roughly 20% of the endogenous proviruses detected in this study were translated into proteins during development in chicken embryo fibroblasts. What these proteins go on to do in the developing bird is not known, say the authors, but it’s an area ripe for study.

Unlike early studies of the endogenous retroviruses in chickens, which studied selected segments of the genome and uncovered only alpha-retroviruses, this study used complete genome sequences and found a great diversity of viral sequences in bird genomes, including the same major groups as those of mammals, including the gamma-, beta-, and spuma-like groups. Most of the endogenous retroviruses in birds were distinct from those found in other animals, probably indicating that the viruses did not move much between different kinds of hosts.

Birds were an early melting pot for viruses

Since endogenous retroviruses are carried from one generation of animal to the next and the age of a provirus can roughly be judged from the number of mutation “errors” it carries, they can provide insights into how both hosts and viruses have evolved over the eons. “Retroviruses leave an integrated DNA copy of their former selves in our genomes,” says Goff. “The genome is a track record of all these infections,” he continues, “they really are a window into the evolutionary path.”

The analysis by Bolisetty et al. of the endogenous retroviruses in bird genomes reveals that millions of years ago birds were host to many different kinds of endogenous retroviruses, serving as a kind of melting pot: a meeting and mingling place where viruses recombined and shared genetic information.

Goff says genome-level studies are a boon for virologists. “This paper is filling a big gap in our understanding of these viruses,” says Goff. “This is something that needed to be done, and advancing sequencing technology made it easy to do.”