Mystery virus found with mostly unknown DNA

The origin and phylogeny of the Yaravirus are not yet clear.

Mystery virus found with mostly unknown DNA
Image source: Rost9/Shutterstock/Big Think
  • A virus has been found whose DNA is 90% absolutely unfamiliar.
  • Scientists have no real idea what it developed from, or how.
  • Viruses used to be thought of as simple, jumbles of things — not so much any more.

In Lake Pampulha in the Brazilian city of Belo Horizonte, scientists found an amoeba virus unlike anything seen before. Named after Yara, the mother of waters in Brazilian mythology, 90 percent of the Yaravirus's genome is comprised of genes never before described. Sifting through the publicly available database of 8,535 metagenomes produced nothing like it, and only 6 of its genes seem to be distantly related to known homologs.

While "most of the known viruses of amoeba have been seen to share many features that eventually prompted authors to classify them into common evolutionary groups," according to the researchers in a preprint paper, Yaravirus is "a new lineage of amoebal virus with a puzzling origin and phylogeny."

Not so simple after all

size comparison chart of common viruses and bacteria

Giant viruses compared in size to to other common viruses and bacteria

Image source: Meletios Verras/Shutterstock

The recent discovery of "giant viruses" — a group to which Yaravirus doesn't belong — has revealed that the organisms are capable of things previously thought beyond their reach.

To begin with, the giant variety is roughly 10 times larger than, say, the influenza virus. With that size comes complexity, too — the flu virus has 11 genes, while a giant virus can have as many as 2,500. And that complexity has turned thinking about viruses on its head.

Conventional wisdom had been that viruses were relatively disorganized agglomerations of stray genetic material incapable of reproduction, and thus dependent on host cells for sustenance. It was previously believed that hijacking their host's metabolisms was the only way that they could survive, and that they were so incredibly simple that they weren't universally considered to be "alive."

Giant viruses, which derive their name from their oversized protein shell or capsid, have genomes complex enough to engage in the synthesis of proteins. They are also capable of DNA repair, replications, transcription, and translation, which has changed the way scientists think about these supposedly simple organisms.

For the scientists who found the Yaravirus, virologists Bernard La Scola from Aix-Marseille University in France and Jônatas S. Abrahão from Brazil's Federal University of Minas Gerais, the discovery is just the latest enigmatic virus they've discovered. Last year, they found a pair of giant viruses (two other viral outliers) which they named as two flavors of Tupanvirus: Tupanvirus soda lake and Tupanvirus deep ocean, each after the extreme aquatic environments in which they were found. They belong to the Mimiviridae virus family, shown above.

But Yaravirus...

Lake Pampulha, where Yaravirus was found

Image source: Teófilo Baltor

Yaravirus represents the latest surprise in viruses, but it's not a giant virus —it's comprised of small particles about 80 nm in size. It's simply that its genome is so novel.

The paper notes, "Using standard protocols, our very first genetic analysis was unable to find any recognizable sequences of capsid or other classical viral genes in Yaravirus [our emphasis]." This leaves authors LaScola and Abrahão no option but to guess what it is. They suggest that it's likely to be the first found example of some unknown amoeba virus group, or perhaps a much-degraded version of some unknown giant virus. They can only conclude, "The amount of unknown proteins composing the Yaravirus particles reflects the variability existing in the viral world and how much potential of new viral genomes are still to be discovered."

A landslide is imminent and so is its tsunami

An open letter predicts that a massive wall of rock is about to plunge into Barry Arm Fjord in Alaska.

Image source: Christian Zimmerman/USGS/Big Think
Surprising Science
  • A remote area visited by tourists and cruises, and home to fishing villages, is about to be visited by a devastating tsunami.
  • A wall of rock exposed by a receding glacier is about crash into the waters below.
  • Glaciers hold such areas together — and when they're gone, bad stuff can be left behind.

The Barry Glacier gives its name to Alaska's Barry Arm Fjord, and a new open letter forecasts trouble ahead.

Thanks to global warming, the glacier has been retreating, so far removing two-thirds of its support for a steep mile-long slope, or scarp, containing perhaps 500 million cubic meters of material. (Think the Hoover Dam times several hundred.) The slope has been moving slowly since 1957, but scientists say it's become an avalanche waiting to happen, maybe within the next year, and likely within 20. When it does come crashing down into the fjord, it could set in motion a frightening tsunami overwhelming the fjord's normally peaceful waters .

"It could happen anytime, but the risk just goes way up as this glacier recedes," says hydrologist Anna Liljedahl of Woods Hole, one of the signatories to the letter.

The Barry Arm Fjord

Camping on the fjord's Black Sand Beach

Image source: Matt Zimmerman

The Barry Arm Fjord is a stretch of water between the Harriman Fjord and the Port Wills Fjord, located at the northwest corner of the well-known Prince William Sound. It's a beautiful area, home to a few hundred people supporting the local fishing industry, and it's also a popular destination for tourists — its Black Sand Beach is one of Alaska's most scenic — and cruise ships.

Not Alaska’s first watery rodeo, but likely the biggest

Image source: whrc.org

There have been at least two similar events in the state's recent history, though not on such a massive scale. On July 9, 1958, an earthquake nearby caused 40 million cubic yards of rock to suddenly slide 2,000 feet down into Lituya Bay, producing a tsunami whose peak waves reportedly reached 1,720 feet in height. By the time the wall of water reached the mouth of the bay, it was still 75 feet high. At Taan Fjord in 2015, a landslide caused a tsunami that crested at 600 feet. Both of these events thankfully occurred in sparsely populated areas, so few fatalities occurred.

The Barry Arm event will be larger than either of these by far.

"This is an enormous slope — the mass that could fail weighs over a billion tonnes," said geologist Dave Petley, speaking to Earther. "The internal structure of that rock mass, which will determine whether it collapses, is very complex. At the moment we don't know enough about it to be able to forecast its future behavior."

Outside of Alaska, on the west coast of Greenland, a landslide-produced tsunami towered 300 feet high, obliterating a fishing village in its path.

What the letter predicts for Barry Arm Fjord

Moving slowly at first...

Image source: whrc.org

"The effects would be especially severe near where the landslide enters the water at the head of Barry Arm. Additionally, areas of shallow water, or low-lying land near the shore, would be in danger even further from the source. A minor failure may not produce significant impacts beyond the inner parts of the fiord, while a complete failure could be destructive throughout Barry Arm, Harriman Fiord, and parts of Port Wells. Our initial results show complex impacts further from the landslide than Barry Arm, with over 30 foot waves in some distant bays, including Whittier."

The discovery of the impeding landslide began with an observation by the sister of geologist Hig Higman of Ground Truth, an organization in Seldovia, Alaska. Artist Valisa Higman was vacationing in the area and sent her brother some photos of worrying fractures she noticed in the slope, taken while she was on a boat cruising the fjord.

Higman confirmed his sister's hunch via available satellite imagery and, digging deeper, found that between 2009 and 2015 the slope had moved 600 feet downhill, leaving a prominent scar.

Ohio State's Chunli Dai unearthed a connection between the movement and the receding of the Barry Glacier. Comparison of the Barry Arm slope with other similar areas, combined with computer modeling of the possible resulting tsunamis, led to the publication of the group's letter.

While the full group of signatories from 14 organizations and institutions has only been working on the situation for a month, the implications were immediately clear. The signers include experts from Ohio State University, the University of Southern California, and the Anchorage and Fairbanks campuses of the University of Alaska.

Once informed of the open letter's contents, the Alaska's Department of Natural Resources immediately released a warning that "an increasingly likely landslide could generate a wave with devastating effects on fishermen and recreationalists."

How do you prepare for something like this?

Image source: whrc.org

The obvious question is what can be done to prepare for the landslide and tsunami? For one thing, there's more to understand about the upcoming event, and the researchers lay out their plan in the letter:

"To inform and refine hazard mitigation efforts, we would like to pursue several lines of investigation: Detect changes in the slope that might forewarn of a landslide, better understand what could trigger a landslide, and refine tsunami model projections. By mapping the landslide and nearby terrain, both above and below sea level, we can more accurately determine the basic physical dimensions of the landslide. This can be paired with GPS and seismic measurements made over time to see how the slope responds to changes in the glacier and to events like rainstorms and earthquakes. Field and satellite data can support near-real time hazard monitoring, while computer models of landslide and tsunami scenarios can help identify specific places that are most at risk."

In the letter, the authors reached out to those living in and visiting the area, asking, "What specific questions are most important to you?" and "What could be done to reduce the danger to people who want to visit or work in Barry Arm?" They also invited locals to let them know about any changes, including even small rock-falls and landslides.

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