BGSU Researcher: More Ancient Viruses Lurk in Our DNA Than We Thought

Newswise — One whole endogenous retrovirus genome — and bits of at least 17 others — were spotted in a study of 2,500 human genomes

Think your DNA is all human? Think again. And a new discovery suggests it’s even less human than previously thought.

In our recent study, we identified 19 “new” pieces of DNA — left by retroviruses that first infected our ancestors’ germlines hundreds of thousands of years ago –lurking between our own genes.

One of these stretches of newfound DNA, detected in ~50 of the ~2,500 people studied, contains an intact, full genetic recipe for an entire virus, raising the possibility of retained functions from this element. It’s only the second intact provirus found to be hiding in human DNA. Our findings were published in the Proceedings of the National Academy of Sciences. As co-first author, I worked with senior author and virologist John Coffin, Ph.D., of the Tufts University School of Medicine, co-first author Zachary Williams, a doctoral student at Tufts, and University of Michigan human genetics researcher Jeffrey Kidd, Ph.D., also a senior author on the work.

Whether or not it can replicate, or generate new viruses, it isn’t yet known. But other studies of ancient virus DNA have shown it may affect the humans who carry it. In addition to finding these new stretches, we confirmed 17 other pieces of virus DNA found in human and archaic genomes by other scientists in recent years.

The study looked at the entire span of DNA, or genome, from people from around the world, including a large number from Africa -- where the ancestors of modern humans originated before migrating around the world. The team used sophisticated techniques to compare key areas of each person’s genome to the “reference” human genome.

The findings add to what science already knows about human endogenous retroviruses, or HERVs –the ancient infectious viruses that inserted a copy of their own genetic material into our ancestors’ genomes. As retroviruses, they are distantly related to the same type of virus that includes the modern human immunodeficiency virus, the cause of AIDS. The new HERVs are part of the family called HERV-K. The intact whole viral genome, or provirus, just found was on the X chromosome; it’s been dubbed Xq21.

Over generations, the genetic copy of the HERVs kept getting copied, as a part of our genome, and handed down to offspring when humans reproduced. In fact, over 8 % of what we think of as our “human” DNA actually came from these very viruses. In some cases, HERV sequences have even been adopted by the human body to serve a useful purpose, such as one, dubbed ‘syncytin’that helps pregnant women’s bodies build a cell layer around a developing fetus to protect it from toxins in the mother’s blood.

This discovery will open up many doors to research and our understanding of genome evolution. What’s more, we have confirmed in this paper that we can use genomic data from multiple individuals compared to the reference human genome to detect new HERVs.

Many of the genomes examined were from the 1000 Genomes Project, an international collaboration. Another set of genomes came from work Kidd and colleagues at Stanford University had done as part of the Human Genome Diversity Project, with a focus on DNA samples from African volunteers.

These latter samples showed more signs of HERVs, in line with the high level of genetic diversity in African populations. That diversity stems from the longtime stability and intermixing of the continent’s population — as opposed to other populations in Europe, Asia and the Americas that stem from specific out-migrations in ancient times.

Cataloging all the HERV insertions in humans will require even more scanning of whole human genomes, which are becoming easier to come by as technology improves and becomes less expensive. And although intact proviruses lurking in our DNA may be rare, the impact of other HERV sequences on our health or disease is probably not.

The research was funded by the National Institutes of Health as well as the American Cancer Society and the F.M. Kirby Foundation.Julia Wildschutte, Ph.D., is a Bowling Green State University Assistant Professor in biological sciences. For more information, go to BGSU.edu. This article is adapted from a publication produced by the University of Michigan.