The researchers at Oxford University and Plymouth University compared genetic data from fossils of Neanderthals and another group of ancient human ancestors called Denisovans to data from modern-day cancer patients.
They found evidence of Neanderthal and Denisovan viruses in the modern human DNA, suggesting that the viruses originated in our common ancestors more than half a million years ago.
This latest finding, reported in journal Current Biology, will enable scientists to further investigate possible links between ancient viruses and modern diseases including HIV and cancer.
"I wouldn't write it off as "junk" just because we don't know what it does yet," said Dr Gkikas Magiorkinis, an MRC Fellow at Oxford University's Department of Zoology.
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"Under certain circumstances, two "junk" viruses can combine to cause disease - we've seen this many times in animals already. ERVs have been shown to cause cancer when activated by bacteria in mice with weakened immune systems," said Magiorkinis.
"How HIV patients respond to HML2 is related to how fast a patient will progress to AIDS, so there is clearly a connection there," said Magiorkinis, study author.
"HIV patients are also at much higher risk of developing cancer, for reasons that are poorly-understood. It is possible that some of the risk factors are genetic, and may be shared with HML2. They also become reactivated in cancer and HIV infection, so might prove useful as a therapy target in the future," Magiorkinis said.
Combining evolutionary theory and population genetics with cutting-edge genetic sequencing technology, they will test if these viruses are still active or cause disease in modern humans.