The Oldest Virus Ever Sequenced Comes From a 7,000-Year-Old Tooth

It seems to belong to an extinct lineage of hepatitis B.

A microscope image of orange hepatitis B particles
A microscope image of hepatitis B particles (in orange)  (CDC / Dr. Erskine Palmer)

Seven thousand years ago, in a valley that is today central Germany, a young man lay down to die. He was 25 or 30, and a farmer most likely. It is not known why he died young. But powerful genetic tools have now pulled out a tantalizing clue: the fragmented DNA of a virus that infected his liver all those millennia ago.

It is the oldest virus ever directly sequenced, opening up a new window onto prehistory. For the past decade or so, ancient human DNA from millennia-old teeth and bones has been revolutionizing the study of the past. More recently, DNA from ancient bacteria—such as leprosy and plague—in those same teeth and bones has done the same for the study of past epidemics. Viruses were always the next logical step. But their genomes are small and sometimes structured in a way that does not hold up well over time.

Until this week, no one had directly sequenced a virus more than a few hundred years old. And now—as a testament to how quickly the field of ancient DNA is moving—not one but two separate research groups report finding hepatitis B viruses in teeth several millennia old in Eurasia.

The first group, led by Ben Krause-Kyora and Johannes Krause in Germany, sequenced viruses from the 7,000-year-old man a well as a 5,000-year-old man and another 1,000-year-old man. Their work is reported in a preprint on bioRxiv, a site where researchers share early versions of papers that have not yet been peer reviewed. A second paper from another group of researchers led by Eske Willerslev at the University of Copenhagen, published in Nature, reports the hepatitis B sequences of 12 individuals ranging from the Bronze Age (2500 B.C.) to the Medieval period. Hepatitis B infects the liver, but it also enters the bloodstream, circulating through the body and winding up in bones and teeth, where it can be preserved.

The millennia-old hepatitis B viruses were all very strange. They looked less like modern-day human viruses than the hepatitis B viruses that today infect chimpanzees and gorillas in Africa. This was true for not just one or two but five hepatitis B viruses across the two studies—found in people living from Germany to Poland, from 7,000 to 3,800 years ago. Whatever version of hepatitis B infected western Europe thousands of years ago seems to have since gone extinct in humans—but lived on in African chimps and gorillas. But was it humans who infected primates with that virus? Or vice versa? And where in the world did it cross over?

Meanwhile, similarly ancient hepatitis B viruses from central Asia resemble viruses found in humans today everywhere from western Europe to the Caribbean to western Africa, according to Willerslev’s study. What makes these so different from the viruses infecting people at the same time in western Europe?

“The papers are really interesting,” says Margaret Littlejohn, a virologist at the Doherty Institute who has studied the origins and evolution of the hepatitis B virus. “But we felt they’re giving us more questions than answers.”

Ancient human DNA also caused a similar state of confusion, initially. The evidence confounded a tidy out-of-Africa hypothesis, in which humans left Africa and sequentially moved through the rest of the continents. In fact, ancient human DNA has revealed, different populations may have left Africa at different times and perhaps even returned. And in most places on Earth, the people who live there have been serially replaced by other groups, over and over. Other populations met dead ends and went extinct. The same appears to have happened with hepatitis B.

The truly surprising takeaway, says Krause-Kyora, an author on one of the studies, is how diverse old hepatitis B lineages once were. The virus has only a fraction of that diversity today.

Willerslev, the lead author on the other study, suggested that this past diversity may be a clue for scientists trying to predict what could happen with hepatitis B in the future. “It provides a catalog of possible mutations this virus has had that have been viable in the past, and obviously some of those mutations could come back,” he said at a press briefing. The prevalence of hepatitis varies widely across the world (ranging from 0.01 percent in the United Kingdom to 22.38 percent in South Sudan), but in total, complications arising from it kill nearly 900,000 people a year.

It might even be possible eventually, says Hendrik Poinar, an ancient DNA researcher who was not involved in the studies, to resurrect these ancient hepatitis B viruses and test them in mice to see exactly how they affected the body. Were the ancient viruses more virulent? Or milder? Did they have a different course of disease entirely?

Both Willerslev’s and Krause-Kyora’s teams chose to study hepatitis B for the same reasons: The virus’s genetic material is composed of DNA rather than RNA, which makes it possible to detect through standard ancient DNA sequencing methods. And it is a chronic infection, meaning the virus stays in the body—including the bones and teeth that ancient DNA researchers study.

But they now have other viruses in sight: herpes, adenoviruses that cause colds, poxviruses. It takes some extra work to extract viral genomes, but bits of viral DNA have been present in what Willerslev calls the “waste product” of ancient sequences all along. When scientists sequence ancient DNA, they actually sequence all of the DNA in a sample—human, bacterial, viral—in one fell swoop. Then they put the fragmented DNA pieces together like a jigsaw puzzle. If you’re only interested in human DNA, that means discarding the bacterial and viral stuff. Now scientists are realizing the “waste product” may hold insights, too. If human DNA can reveal who the long-dead are, pathogen DNA can reveal how they lived, how they suffered, and perhaps how they died. It may also reveal contacts between populations that exchanged diseases but did not interbreed.

Willerslev says they are now going back and looking for pathogens in the old samples they had analyzed only for human DNA. “I can say 10 percent of the samples of the individuals have kind of nasty pathogens ... when we use teeth you also find some 50 percent of individuals have all kinds of oral infection that you might not die of but is not nice to have,” he says. “The picture that emerges from this line of work is that a lot of people were running around with diseases in the past. And it certainly kind of cracked my romantic picture of the Bronze Age.”