Nineteen previously unidentified pieces of non-human DNA — left by retroviruses that first infected human ancestors hundreds of thousands of years ago — have been found by scientists in a study of 2,500 human genomes. According to the team, one stretch of newfound DNA, found in about 50 of the 2,500 genomes studied, contains an intact ancient virus – only the second such virus described.
This electron micrograph shows particles of a provirus resurrected from human DNA in 2006. Scale bar – 200 nm. Image credit: Marie Dewannieux et al.
The findings, published online in the Proceedings of the National Academy of Sciences, add to what researchers already know about human endogenous retroviruses (HERVs). That’s the name for the ancient infectious viruses that inserted a DNA-based copy of their own RNA genetic material into the genomes of human ancestors.
They’re part of the same type of virus that includes the modern human immunodeficiency virus, which causes AIDS.
Over generations, the virus-generated DNA kept getting copied and handed down when humans reproduced. That’s how it ended up in our DNA today.
In fact, HERVs have contributed to more than 8% of the human genome. In some cases, HERV sequences have been adopted by the human body to serve a useful purpose, such as one that helps pregnant women’s bodies build a cell layer around a developing fetus to protect it from toxins in the mother’s blood.
The new HERVs are part of the endogenous retrovirus family called HERV-K.
The intact whole viral genome — named the provirus Xq21 — just found was on the X chromosome. It’s only the second intact provirus found to be hiding in human DNA.
Whether or not Xq21 can replicate, or reproduce, it isn’t yet known. But other studies of ancient virus DNA have shown it can affect the humans who carry it.
“This is a thrilling discovery. It will open up many doors to research,” said study lead author Dr. Julia Wildschutte, from the University of Michigan Medical School.
Dr. Wildschutte and co-authors looked at the entire span of DNA from people from around the world, including a large number from Africa — where the ancestors of modern humans originated before migrating around the world.
They used sophisticated techniques to compare key areas of each person’s genome to the ‘reference’ human genome.
“What’s more, we have confirmed that we can use genomic data from multiple individuals compared to the reference human genome to detect new HERVs,” Dr. Wildschutte said. “But this has also shown us that some people carry insertions that we can’t map back to the reference.”
In addition to finding the new stretches, the team also confirmed 17 other pieces of virus DNA found in human genomes by other scientists in recent years.
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Julia Halo Wildschutte et al. Discovery of unfixed endogenous retrovirus insertions in diverse human populations. PNAS, published online March 21, 2016; doi: 10.1073/pnas.1602336113
