Scientists have revived a ‘zombie’ virus that spent 48,500 years frozen in permafrost

Researchers have isolated viable microbes from melting permafrost after tens of thousands of years.

Warmer temperatures in the Arctic are thawing the region’s permafrost – a frozen layer of soil beneath the earth – and potentially reviving viruses that have been dormant for tens of thousands of years.

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Ores of Earth drilled from Siberian permafrost have been analyzed to detect frozen viruses. © Jean-Michel Claverie/IGS/CNRS-AMU / Fair Use

while a pandemic caused by a disease from the distant past seems like the premise of a science fiction film, scientists warn that the risks, just minor, are underestimated. During thaws, chemical and radioactive waste from the Cold War may be released, potentially harming species and disrupting ecosystems.

“There’s a lot going on with the permafrost that is of concern, and it really shows why it’s super important that we keep as much of the permafrost frozen as possible,” said Kimberley Miner, a climate scientist at the NASA Jet Propulsion Laboratory at the California Institute of Technology in Pasadena, California.

Permafrost spans one-fifth of the Northern Hemisphere and has long supported the Arctic tundra and boreal forests of Alaska, Canada, and Russia. It acts as a time capsule, preserving the mummified remains of several extinct creatures that scientists have been able to discover and analyze in recent years, including two cave lion cubs and a woolly rhino.

Permafrost is a suitable storage medium not only because it is cold; it is also an oxygen-free environment where light does not penetrate. However, present Arctic temperatures are warming up to four times faster than the rest of the earth, undermining the region’s top layer of permafrost.

Jean-Michel Claverie, an Emeritus professor of medicine and genomics at Aix-Marseille University School of Medicine in Marseille, France, has tested earth samples taken from Siberian permafrost to see if any viral particles contained therein are still infectious. He’s looking for “zombie viruses,” as he calls them, and he’s found some.

The virus hunter

Claverie studies a particular type of virus he first discovered in 2003. Known as giant viruses, they are much bigger than the typical variety and visible under a regular light microscope, rather than a more powerful electron microscope – which makes them a good model for this type of lab work.

His efforts to detect viruses frozen in permafrost were partly inspired by a team of Russian scientists who in 2012 revived a wildflower from a 30,000-year-old seed tissue found in a squirrel’s burrow. (Since then, scientists have also successfully brought ancient microscopic animals back to life.)

In 2014, he managed to revive a virus he and his team isolated from the permafrost, making it infectious for the first time in 30,000 years by inserting it into cultured cells. For safety, he’d chosen to study a virus that could only target single-celled amoebas, not animals or humans.

He repeated the feat in 2015, isolating a different virus type that also targeted amoebas. And in his latest research, published February 18 in the journal Viruses, Claverie and his team isolated several strains of ancient virus from multiple samples of permafrost taken from seven different places across Siberia and showed they could each infect cultured amoeba cells.

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This is a computer-enhanced microphoto of Pithovirus sibericum that was isolated from a 30,000-year-old sample of permafrost in 2014. © Jean-Michel Claverie/IGS/CNRS-AMU / Fair Use

Those latest strains represent five new families of viruses, on top of the two he had revived previously. The oldest was almost 48,500 years old, based on radiocarbon dating of the soil, and came from a sample of earth taken from an underground lake 16 meters (52 feet) below the surface. The youngest samples, found in the stomach contents and coat of a woolly mammoth’s remains, were 27,000 years old.

That amoeba-infecting viruses are still infectious after so long is indicative of a potentially bigger problem, Claverie said. He fears people regard his research as a scientific curiosity and don’t perceive the prospect of ancient viruses coming back to life as a serious public health threat.

“We view these amoeba-infecting viruses as surrogates for all other possible viruses that might be in the permafrost,” Claverie told CNN.

“We see the traces of many, many, many other viruses,” he added. “So we know they are there. We don’t know for sure that they are still alive. But our reasoning is that if the amoeba viruses are still alive, there is no reason why the other viruses will not be still alive, and capable of infecting their own hosts.”

Precedent for human infection

Traces of viruses and bacteria that can infect humans have been found preserved in permafrost.

A lung sample from a woman’s body exhumed in 1997 from permafrost in a village on the Seward Peninsula of Alaska contained genomic material from the influenza strain responsible for the 1918 pandemic. In 2012, scientists confirmed the 300-year-old mummified remains of a woman buried in Siberia contained the genetic signatures of the virus that causes smallpox.

An anthrax outbreak in Siberia that affected dozens of humans and more than 2,000 reindeer between July and August in 2016 has also been linked to the deeper thawing of the permafrost during exceptionally hot summers, allowing old spores of Bacillus anthracis to resurface from old burial grounds or animal carcasses.

Birgitta Evengård, professor emerita at Umea University’s Department of Clinical Microbiology in Sweden, said there should be better surveillance of the risk posed by potential pathogens in thawing permafrost, but warned against an alarmist approach.

“You must remember our immune defense has been developed in close contact with microbiological surroundings,” said Evengård, who is part of the CLINF Nordic Centre of Excellence, a group that investigates the effects of climate change on the prevalence of infectious diseases in humans and animals in northern regions.

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A boat served as a canteen and storage space for the team that took cores that Claverie used in his experiments. © Jean-Michel Claverie/IGS/CNRS-AMU / Fair Use

“If there is a virus hidden in the permafrost that we have not been in contact with for thousands of years, it might be that our immune defense is not sufficient,” she said. “It is correct to have respect for the situation and be proactive and not just reactive. And the way to fight fear is to have knowledge.”

Chances of viral spillover

Of course, in the real world, scientists don’t know how long these viruses could remain infectious once exposed to present-day conditions, or how likely the virus would be to encounter a suitable host. Not all viruses are pathogens that can cause disease; some are benign or even beneficial to their hosts. And while it is home to 3.6 million people, the Arctic is still a sparsely populated place, making the risk of human exposure to ancient viruses very low.

Still, “the risk is bound to increase in the context of global warming,” Claverie said, “in which permafrost thawing will keep accelerating, and more people will populate the Arctic in the wake of industrial ventures.”

And Claverie isn’t alone in warning that the region could become a fertile ground for a spillover event – when a virus jumps into a new host and starts to spread.

Last year, a team of scientists published research on samples of soil and lake sediment taken from Lake Hazen, a freshwater lake in Canada located within the Arctic Circle. They sequenced the genetic material in the sediment to identify viral signatures and the genomes of potential hosts – plants and animals – in the area.

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Cores of permafrost samples are pictured in a container. © Jean-Michel Claverie/IGS/CNRS-AMU / Fair Use

Using a computer model analysis, they suggested the risk of viruses spilling over to new hosts was higher at locations close to where large amounts of glacial meltwater flowed into the lake – a scenario that becomes more likely as the climate warms.

Unknown consequences

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Permafrost thaw can be gradual or happen much more quickly. © Jean-Michel Claverie/IGS/CNRS-AMU / Fair Use

Identifying viruses and other hazards contained in the warming permafrost is the first step in understanding what risk they pose to the Arctic, Miner at NASA’s Jet Propulsion Laboratory said. Other challenges include quantifying where, when, how fast, and how deep permafrost will thaw.

Thawing can be a gradual process of as little as centimeters per decade but also happens more rapidly, such as in the case of massive land slumps that can suddenly expose deep and ancient layers of permafrost. The process also releases methane and carbon dioxide into the atmosphere – an overlooked and underestimated driver of climate change.

Miner cataloged an array of potential hazards currently frozen in Arctic permafrost in a 2021 paper published in the scientific journal Nature Climate Change.

Those possible dangers included buried waste from the mining of heavy metals and chemicals such as the pesticide DDT, which was banned in the early 2000s. Radioactive material has also been dumped in the Arctic – by Russia and the United States – since the advent of nuclear testing in the 1950s.

“Abrupt thaw rapidly exposes old permafrost horizons, releasing compounds and microorganisms sequestered in deeper layers,” Miner and other researchers noted in the 2021 paper.

In the research paper, Miner labeled the direct infection of humans with ancient pathogens released from permafrost as “currently improbable.”

However, Miner said she is worried about what she termed “Methuselah microorganisms” (named after the Biblical figure with the longest life span). These are organisms that could bring the dynamics of ancient and extinct ecosystems into the present-day Arctic, with unknown consequences.

The re-emergence of ancient microorganisms has the potential to change soil composition and vegetative growth, possibly further accelerating the effects of climate change, Miner said.

“We’re really unclear as to how these microbes are going to interact with the modern environment,” she said. “It’s not really an experiment that I think any of us want to run.”

The best course of action, Miner said, is to try and halt the thaw, and the wider climate crisis, and keep these hazards entombed in the permafrost for good.