Viruses do not make good fossils. But advances in genomic technology have allowed scientists to peer into the genetic material of viruses and their hosts to search for clues about their shared evolutionary history.

Genetic code from retroviruses has been found to compose some 8 percent of the human genome, having been copied in during replication and left to be inherited by us and our progeny. But non-retroviral RNA viruses do not use their host's DNA to replicate—and some do not even enter the host cell's nucleus. Nevertheless, new research has turned up surprising evidence that some of these viruses are enmeshed in the genomes of vertebrates—including humans and other mammals.

One of these new studies, published online July 29 in PLoS Pathogens, has uncovered some 80 examples of viral genetic data circulating in the genomes of vertebrate species for the past 40 million years.

To discover these connections, the group ran computer analyses of 5,666 genes from all known non-retroviral, single-stranded RNA virus families against the genomes of 48 vertebrate species. The strongest matches belonged to just two virus groups: Bornaviruses and filoviruses, the latter of which includes the deadly Ebola and Marburg hemorrhagic fever pathogens.

Another recent paper, published January 2010 in Nature, found bornavirus genes in the human genome. (Scientific American is part of Nature Publishing Group.)

Previous research had located evidence of viral fragments in the genomes of plants and insects, but in the past year new findings of these code segments in vertebrates surprised many biologists. "Retroviruses are an enormous fraction of the human genome, but that was a little understandable because the viruses have to inject their material into the DNA to survive," says Anna Marie Skalka, basic science director emeritus at Fox Chase Cancer Center in Philadelphia and co-author of the PLoS Pathogens paper. Otherwise, errant genetic material from viruses that are not retroviruses can find its way into the genome of germ line cells during the RNA copy process. That material can then get spliced into the genome by long interspersed repetitive elements (LINE) that are usually busy copying their own RNA.

When these infrequent flubs happen, they can be beneficial, harmful or neutral, Skalka explains. "There are LINE integrations that cause cancer or you could look at them as providing fodder for evolution—we have more sequences in there that can evolve and eventually make other genes."

Ancient code
Many viruses can undergo incredibly rapid adaptation, eluding immune systems that learn to recognize previous strains. But some researchers are pointing to emerging data on these viral "fossils" as indication that many viruses are in fact ancient—and have changed little since their material was integrated into host genomes.

"Previously there was no way to get an idea of how old they were," Skalka says of these viruses. But like tracing the evolutionary history of other organisms, genomic analysis can give scientists a new way to assess these estimates.

The new findings support a theory of Tufts University School of Medicine molecular biologist John Coffin that viruses in the bornavirus and filovirus groups "are really very old—despite the fact that card-carrying evolutionary biologists have concluded that they must be evolving very rapidly and probably [are] very recent," he says. "That is clearly very wrong." He cites this and other recent work to conclude that some of these hemorrhagic fever viruses have changed little in the course of primate evolution.

This time differential is both exciting to researchers who have been hunting for ancient evidence of the viruses' evolution and challenging to those who are trying to find these viral fossils in contemporary genetic codes.

"It is a big challenge" to match genes from modern viruses with those that might have entered animal genomes millions of years ago," Skalka says. "These RNA viruses evolve very, very rapidly and they change very, very rapidly—so the probability that you could find something that existed 40 million years ago could be very low."

Even though the recent assays have found several firm viral matches, many researchers assume there is likely much more virus material hiding out in our genomes. "All viruses make messenger RNAs, so it seems very possible that many others could have been picked up by LINEs and worked in," Skalka says. The others might be harder to find, however. It is possible that "they've evolved so rapidly that we don't recognize them any more."

8 Comments

1. 1. JamesDavis 07:45 AM 7/30/10

   It sounds like the viruses are allowing us to live on this planet and making sure we can change when the cycles change. A person can't help wondering... ...after all these years, how much of us is actually us? If, over time, we have become a virus, then viruses are pretty darn good looking and nice to snuggle up to during cold weather. Maybe that fever virus allows us to keep warm in cold weather...nice guy to have on our side.

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2. 2. RHill 11:33 AM 7/30/10

   I think it's cool and shows how all life on Earth is rather intimately related.

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3. 3. rshoff 02:28 PM 7/30/10

   We consider ourselves independent from our environment, however it seems that we are not individual units so much as nodes of life mass swimming through a veritable pea soup, churning with our surroundings.

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4. 4. bgilbert 08:08 PM 7/31/10

   Is it possible that some sequences in DNA are used, not for coding proteins, nor regulating the expression of other genes, but as a library of known pathogens for priming the immune system. There would be selective pressure to keep these sequences the same as the pathogen, even tracking the evolution of the pathogen - so even if the sequence got into the genome a long time ago, it would have been updated to match the changes in the pathogen.

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5. 5. jtdwyer 07:22 AM 8/1/10

   I suspect that, once inserted into our predecessors' genome, DNA need not infer any survival benefit as long as it not be a short term detriment to an individual's survival.
   
   Perhaps our DNA not only acts as a reservoir for viral DNA but under some conditions our own DNA spawn our own pathogens.

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6. 6. rbinanth 03:34 PM 8/2/10

   How are you sure that viral DNA is inserting itself into the host genome and not that the host genome is splitting off into viral DNA particles? Perhaps we are making our own viruses?

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7. 7. jtdwyer in reply to rbinanth 04:30 PM 8/2/10

   rbinanth - Good question: I independently had a similar thought preceding your comment...
   
   I'm not well read on the subject, but if I recall normal viral processes insert their DNA into the host's DNA, utilizing its additional function to replicate copies of the virus. But I think the question is still valid: under some conditions could the viral DNA snippet be reactivated, generating new viruses?

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8. 8. jtdwyer 10:00 PM 8/4/10

   The article repeatedly states that there must be some benefit imparted to a host for it to retain DNA for millions of years. As I understand, most of human DNA, for example, is nonfunctional, inferring no characteristic, beneficial or not, to the host. It seems that DNA, once inserted into a genome, must merely not be detrimental to its reproduction in order to be retained. In this way many viruses' RNA could be inserted into a host's genome, accumulating over millions of years unless some process specifically removed it.

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