INFECTIOUS INSERTIONS: Today's songbirds are harboring traces of ancient viral strains in their genomes, giving researchers a new understanding of the disease's age and evolutionary history.
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Viruses can be thought of as hyperspeed shape-shifters, organisms that can adapt quickly to overcome barriers to infection. But recent research has been finding ancient traces of many viruses in animal genomes, DNA insertions that have likely been there for much longer than the viruses were previously thought to have existed at all.
A new study describes evidence of a hepadnavirus (a virus group that includes hepatitis B, which infects humans as well as other mammals and ducks) hiding in the genomes of modern songbirds. By tracing back to these bird species' common ancestors, the researchers behind the new work estimate that this family of viruses has been around for at least 19 million years—and possibly as long as 40 million years—rather than the several thousand years researchers had estimated.
Such a primordial start is difficult to square with how similar these ancient snippets' DNA looks to currently circulating versions of the virus and what we know about viruses' ability to change so rapidly. "It's just something we don't quite grasp in the evolution of viruses," says Cédric Feschotte, an associate professor at the University of Texas Arlington's Department of Biology and co-author of the new study. "I think that's pretty exciting." By complicating the understanding of viral evolution, the new findings also promise to help inform transmission dynamics and the ways in which viruses move among different host species.
The new estimate would slow the average rate of hepadnavirus mutation some 1,000-fold, wrote the researchers of the new the study, published online September 28 in PLoS Biology.
Given the bold new picture of virus evolution that many of this and other recent genomic insertion discoveries imply, however, Feschotte is braced for blowback from the field. But the study's numbers look solid, says Harmit Malik, an evolutionary geneticist at the Fred Hutchinson Cancer Research Center who was not involved in the new research. "There was a fairly high burden of proof" in the study, he says; "I think the authors have done a really good job."
Beyond retro
These so-called viral fossils are not mineralized relics but rather bits of genetic code held over in the genome of a modern-day host organism. Until recently, most known viral genomic insertions came from retroviruses, which use host cells' nuclei to replicate—thereby making accidental incorporation into the host's genome more likely than from viruses that replicate outside of the nucleus. The human genome, for example, is thought to owe some 8 percent of its code to endogenous retroviruses. And a July study, published online in PLoS Pathogens, described dozens of examples of viral code in vertebrate genomes—much of which had likely been there for some 40 million years.
As viruses go, hepadnaviruses are a likely candidate to get mixed up with the host's own genetic material. Hepatitis B, a disease that kills some 600,000 people worldwide each year, replicates using RNA, and bits of the virus's genetic material are frequently found inside a host's liver cells.
In order to have become integrated in bird genomes and be passed along for millions of years, however, these hepadnaviruses would have needed to insert genetic material into the sperm or egg cells of their avian hosts. The authors propose that given the viral fossils' time span and diversity, the insertions likely happened on multiple occasions—possibly over the course of millions of years. Feschotte suggests that it is likely having a bit of the virus's code integrated in a bird's genome might have conferred immune protection against similar viruses.
Different speeds
Modern-day viruses are an extremely diverse bunch. Because of the observed quick mutation rates, however, "you could explain away all the diversity as arising from a common ancestor maybe 10,000 years ago," Malik says.
In studying the molecular changes in these viruses, "you would never predict to see something that is 20 million years old that resembles so closely the circulating ones," Feschotte notes. The location of the insertions, however, suggests that these integrations are not modern flukes.
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9 Comments
Add CommentCuriosity killed the cat.
Reply | Report Abuse | Link to thisWouldn't the genetic survival of an endogenous retrovirus depend not only on its ability to replicate (with host assistance), but the ability of the host to replicate, or at least not die too fast? As a result, might not many retrovirus mutations result in death of the host before the retrovirus could be replicated? This might reduce the mutation rate in the host population.
Reply | Report Abuse | Link to thisIf the host exhibits a latent infection it would probably survive unless a change in environment or health caused a shift to a productive infection. With latent, provirus would emerge in offspring.
Reply | Report Abuse | Link to thisThat's the standard process, but the behavior of mutations could be unpredictable.
Reply | Report Abuse | Link to thisAs is in life. All mutations are unpredictible. One thing this does prove is genetic code can be transfered from generation to generation. This might help other research goals in determining alcoholism, addiction behavior that is passed on. These all are in the genome. Great article.
Reply | Report Abuse | Link to thisI think Cédric Feschotte, can close his eyes, toss a dart, and any information he comes up with about viruses will probably be correct. The more exotic you are, the more correct you become. What I have always found interesting in speculating about viruses is; Is the virus rapidly mutating its self so it can live in the host or is the virus rapidly mutating the host and slowly turning the host into a virus so their can be cohabitation? Any time you do anything to living DNA, there is a rapid response and effect. If you could determine if viruses have a gender, wouldn't it be interesting to see what gender virus you have in you?
Reply | Report Abuse | Link to thisInteresting article...parts of it confuse me...if a virus inserts its DNA into the hosts DNA(sperm or egg)...does that mean that its offspring create viruses...not stating this very well...if I have this segment of DNA in my cells passed down to me from my parents...do I create the virus in my cells....
Reply | Report Abuse | Link to thisInteresting article on many levels:
Reply | Report Abuse | Link to this1. The degree to which "infectious agents" (in this case viruses) shape evolutionary change.
2. THe amount of the human or mammalian genome represented by viral DNA.
The fact of the matter is we are dependent upon and evolved to be carriers of a veritible Universe of Microbes: Intelligent Design... um, I think not.
Viral infection usually tends to be a limited acute, non-lethal phase followed by either chronic low-grade infection of viral reproduction or a chronic carrier state. Hepatitis B is a classic example and only a minority eventually succumb to liver failure or hepatic cancer... while many more are carriers.
But on a far more basic level, the human placenta is utterly dependent on viral DNA for normal function! The only difference between us and our primate pals is the degree of invasion of the trophoblastic cells of this hemo-choriol unit (into the uterine decidua)... which allows it to supply the very metabolically demanding, devoloping homo sapien brain. (regulated by our high levels of glycosylated HCG.... but that's not really germane here.)
Anyway, we are all, from plants to animals, apart of this whacky, wonderful evolving Cosmos... so, enjoy the ride and don't be a germaphobe!