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Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology



Matthieu Legendre, Julia Bartoli, Lyubov Shmakova, Sandra Jeud, Karine Labadie, Annie Adrait, Magali Lescota, Olivier Poirota, Lionel Bertauxa, Christophe Bruley, Yohann Couté, Elizaveta Rivkina, Chantal Abergel, and Jean-Michel Claverie




Cтатья еще не вышла в свет, но журналисты из РИА-новости уже оповестили весь мир об этом....
РИА Новости

Российские ученые нашли гигантский вирус в древней мерзлоте на Колыме


Это первая находка гигантского вируса в мерзлоте. В процессе постоянного разрушения берегов, сложенных мерзлыми отложениями, в реки и океан попадают законсервированные в мерзлоте жизнеспособные микроорганизмы, включая и гигантские вирусы, которые встраиваются в современные экосистемы.
Ученые обнаружили в сибирской мерзлоте возрастом более 30 тысяч лет жизнеспособный гигантский вирус, паразитирующий на амебах, говорится в статье в журнале Proceedings of the National Academy of Sciences.
Ученые обнаружили рекордного "родственника" гигантского вируса
Елизавета Ривкина, заведующая лабораторией криологии почв Института физико-химических и биологических проблем почвоведения в Пущино, и старший научный сотрудник этой лаборатории Любовь Шмакова вместе с французскими коллегами под руководством доктора Жан-Мишеля Клаверье из Марсельского института микробиологии исследовали образцы мерзлоты, отобранные в районе Колымской низменности, которые хранятся в лаборатории криологии почв.
Ученым уже известны гигантские вирусы, которые по размеру сопоставимы с бактериями. Все они паразитируют на свободноживущих амебах. Первый из таких вирусов, названный мимивирусом, был открыт Клаверье и его коллегами в 2003 году, до тех пор ученые не подозревали о том, что существуют такие большие вирусы. После этого были найдены еще несколько гигантских вирусов. В ходе совместной работы ученые заражали акантамеб, выделенных Шмаковой из вечной мерзлоты, мегавирусами, открытыми французскими учеными.
Елизавета Ривкина: "Оказалось, что амебы из сибирской мерзлоты возрастом более 30 тысяч лет устойчивы к мегавирусам, которые паразитируют на амебах, выделенных из современных экосистем. В ходе работы из древней мерзлоты был выделен новый гигантский вирус, названный Pithovirus sibericum. На сегодняшний день это самый большой описанный вирус. Кроме того, он является представителем нового семейства гигантских амебных вирусов. Он и описан в нашей статье".
Это первая находка гигантского вируса в мерзлоте. В процессе постоянного разрушения берегов, сложенных мерзлыми отложениями, в реки и океан попадают законсервированные в мерзлоте жизнеспособные микроорганизмы, включая и гигантские вирусы, которые встраиваются в современные экосистемы, однако для человека они безопасны, так как паразитируют только на амебах.
Ривкина отметила интересный способ "охоты" гигантских вирусов на амеб: вирусы "завлекают" их, "прикидываясь вкусной бактерией". Амеба, поглощая "наживку", становится жертвой вируса, превращаясь в "фабрику" по производству его новых копий.
"Основным объектом наших исследований являются микроорганизмы, сохранившиеся в мерзлоте возраста от нескольких тысяч до нескольких миллионов лет. Непосредственно с вирусами мы не работаем" — пояснила Ривкина.



Беседа Елизаветы Михайловны на радио BBC с Севой Новгородцевым:





National Geographic

By Stefan Sirucek for National Geographic

PUBLISHED MARCH 3, 2014

Buried deep in the Siberian permafrost and untouched for over 30,000 years, researchers have discovered what is thought to be the newest representative of what are loosely known as "giant viruses."


A team led by Jean-Michel Claverie and Chantal Abergel of Aix-Marseille University in Marseille, France, made the discovery of the previously unknown virus, which has been dubbed Pithovirus sibericum and can be revived in the lab.

Their findings are detailed in a new article in the Proceedings of the National Academy of Sciences.

Lest Siberian excavation makes you think of frozen woolly mammoths, make no mistake: These giants are still decidedly microscopic. But in the diminutive world of viruses they're larger than normal specimens, measuring 1.5 microns in length and 0.5 microns in diameter. The pandoraviruses, the largest viruses previously discovered, also by the team of Claverie and Abergel, measure 1 micron in length and 0.5 in diameter.

"'Giant' viruses are loosely defined as the ones that you can see under a regular microscope," explained Claverie and Abergel when contacted via email.

Large and Complex

Giant viruses also dwarf other viruses in terms of genetic complexity. The newly discovered Pithovirus contains 500 genes, and the aforementioned Pandoravirus can contain up to 2,500.

For comparison, the HIV virus contains only about 12 genes, explained James Van Etten, a professor of plant pathology at the University of Nebraska, when reached for comment. (Van Etten is an authority on viruses and edited the new study.)

Amazingly, even after more than 30,000 years embedded in ancient permafrost, when Claverie and Abergel exposed amoebas in their lab to the virus, they found that the virus was still active and quickly infected the host cell. "We use amoeba on purpose as a safe bait for capturing viruses. We then immediately verify that they are not able to infect animal/human cells," stressed the researchers.

Giant viruses are not just bigger but are hardier than others as well, said the researchers. This hardiness, along with a favorable environment, likely helped the newly discovered specimen stay intact for the thousands of years that it did. Viruses are often destroyed or rendered inactive by a number of factors, including light and biochemical degradation.

"Among known viruses, the giant viruses tend to be very tough, almost impossible to break open," said Claverie and Abergel. "Special environments such as deep ocean sediments and permafrost are very good preservers of microbes [and viruses] because they are cold, anoxic [lacking oxygen], and in the dark."

Intricate and Varied

The past decade has seen something of a renaissance in the discovery of large, genetically complex viruses, with the discovery of three distinct groups (Mimivirus, Pandoravirus, and now Pithovirus) suggesting that viruses can be much more intricate and varied than previously thought, and that giant viruses may not be especially uncommon.

The newly discovered diversity in genetic makeup and morphology among viruses leads Van Etten to surmise that different types of viruses may have evolved separately.

"The idea that all viruses evolved from one common origin, I suspect is not true," said Van Etten.

Changing Climate: Growing Threat?

If long-buried viruses can be unearthed, what else might be capable of coming to the surface? Climate change as well as industrial activities may shake up the ancient ice enough to bring potential pathogens to the surface.

"Mining and drilling means ... digging through these ancient layers for the first time in millions of years. If 'viable' [viral particles] are still there, this is a good recipe for disaster," said Claverie and Abergel.

But Edward Mocarski, a professor of microbiology at Emory University, says the risk of a virus pathogenic to humans being released from the ice is very small.

"The idea would make a great movie but is extremely unlikely unless the virus came from a frozen human being who possibly died from a virus that is no longer in circulation," said Mocarski when contacted via email.

"A very small proportion [of the viruses on Earth] represent viruses that can infect mammals and an even smaller proportion pose any risk to humans."

University of Nebraska's Van Etten agreed that such a situation was unlikely but possible with the right conditions.

"The biggest source of genes on the planet is probably from viruses, and they're just everywhere, but in general they're highly specific for the organisms that they grow in," said Van Etten.

The researchers behind the discovery, Claverie and Abergel, believe that whether or not it's likely, such a scenario remains feasible. They counsel vigilance and continued testing. As their latest research has shown, large DNA viruses may remain infectious for very long stretches of time.

"The fact that we might catch a viral infection from a long-extinct Neanderthal individual is a good demonstration that the notion that a virus could be 'eradicated' from the planet is plain wrong and gives us a false sense of security. At least a stock of vaccine should be kept, just in case," said Claverie and Abergel.

Their research will now turn to assessing how real a threat these ancient viruses pose.

"We are now doing more work to analyze the DNA content of these permafrost layers in a search for the genetic signature of viruses resembling human pathogens," said Claverie and Abergel, who stressed that they are not attempting to "revive" any such pathogenic viruses, but rather hoping to determine the potential danger.

"If we find some [human pathogens], then the risk will become more real. If not, we will be safe."



The New Zealand Gerald:

Scientists revive 30,000-year-old virus in Siberia


11:00 AM Wednesday Mar 5, 2014

The discovery of an infectious giant virus that had been entombed in Siberian permafrost for 30,000 years has led scientists to warn of other disease-causing viruses and microbes that may escape from the frozen earth once it has melted.

Scientists in France and Russia discovered the giant virus in samples of frozen earth taken from the far north-east of Russia. Tests in the laboratory showed that the virus was capable of infecting amoeba - single-celled micro-organisms - although it cannot infect multi-cellular animals and humans.

The virus is much larger than usual viruses and is so big it can be seen under ordinary optical microscopes. It is similar to two other known types of giant viruses, but its genetic material is different enough for it to be classified as belonging to a distinct species, Pithovirus sibericum, within a totally new group of viruses.

Researchers at the Russian Academy of Sciences in Pushchino
and France's National Centre for Scientific Research (CNRS) in Marseille said that the virus was buried 30 metres (100 feet) below ground in the Chukotka autonomous region of Siberia and must have been frozen for at least 30,000 years before it burst back into life when offered the "bait" of living amoeba in a laboratory experiment.

"This study demonstrates that viruses can survive in permafrost - the permanently frozen layer of soil found in the Arctic regions - almost over geological time periods, that is for more than 30,000 years," a CNRS spokeswoman said.

"These findings have important implications in terms of public-health risks related to the exploitation of mining and energy resources in circumpolar regions, which may arise as a result of global warming," she said.

"The re-emergence of viruses considered eradicated, such as smallpox, whose replication process is similar to Pithovirus, is no longer the domain of science fiction. The probability of this type of scenario needs to be estimated realistically," she added.

The virus was last active at a time when mammoths roamed the Siberian steppes and the last Neanderthals were on the verge of extinction in the Iberian peninsula. The virus particle survived by being encased in a protective protein coat, measuring 1.5 thousandths of a millimetre long.

The giant Pithovirus replicates inside the part of the amoeba that lies outside its cell's nucleus. This form of cytoplasmic replication is similar to the way large DNA virus replicate, including the Variola virus which causes smallpox.

Chantal Abergel, a CNRS scientist who helped to carry out the work, said that there may be other viruses frozen in the permafrost layers of the Arctic that could become active again when disturbed either by drilling or by the melting of the frozen ground.

"It may be possible to find other viruses that may be able to infect other kinds of host organisms other than amoeba. We need really to study the DNA of permafrost samples to directly study the kind of microbes that exist there," Dr Abergel said.

"We don't know what is there in the permafrost but we need to be careful when prospecting for oil, minerals or whatever we are looking for. The message should be 'think before you drill'. And if someone does get sick on the spot, the last thing is to send them back immediately to New York or London or any other city where a virus infection can spread," she said.

The Pithovirus, which is named after the Greek word to describe the amphora handed by the gods to Pandora, was found by drilling horizontally half way down a 60 metre cliff formed by the River Anyuy in the Kolyma region of Siberia.

The lead researchers in Russia were Lyubov Shmakova and Elizaveta Rivkina of the Institute of Physicochemical and Biological Problems in Soil Science in Pushchino.



Newscientist:


20:00 03 March 2014 by Andy Coghlan

Biggest-ever virus revived from Stone Age permafrost




As if there weren't enough problems with thawing tundra. A virus of unprecedented size has been isolated from Russian permafrost 30,000 years old and reactivated.

Dubbed a pithovirus after the Greek pithos, meaning a large earthenware jar like an amphora, the virus infects amoebas but does not appear to harm human or mouse cells.

Even so, now that this virus has been revived from the permafrost, so too could potentially harmful pathogens, possibly including viruses humans have never encountered before, the researchers say.

"There's good reason to think there could be pathogenic viruses in there too," says Chantal Abergel of Aix-Marseille University in Marseille, France, and co-leader of the team that discovered the virus.

Mining risk

"Thirty percent of the world's oil reserves are thought to be hidden under the permafrost, along with gold and other key minerals, so exploration is bound to increase," says Jean-Michel Claverie, co-leader of the team. "So we must be careful to take precautions when prospecting – if people become sick with strange symptoms, it might be wise to quarantine and clear them of dangerous new infections before sending them back," he says.

The pithovirus itself is very different from any known virus. At 1.5 micrometres long by 0.5 micrometres wide, it is around 30 per cent bigger than what had been the largest known virus – the pandoravirus, also found by Claverie's team.

Yet despite being physically larger, the pithovirus has only a fifth as many genes as the 2500 in the pandoravirus. The two giant viruses share just five genes.

Reviving the pithovirus needed no sophisticated techniques. Rather, Claverie and Abergel "baited" the peat-like permafrost sample with amoebas. "We used the amoebas to draw out the virus, as we know these giant viruses tend to infect amoebas," says Claverie.

Invasion filmed

The researchers tracked and filmed the pithovirus's entire life cycle. Once inside an amoeba, it migrates to the wall of a chamber called a vacuole. It does this with the help of an unusual structure at one end that the team discovered, which serves as a kind of cork.

"Its function is to seal and protect the amphora-shaped particle, but as soon as it enters a vacuole, the cork is removed to initiate the infection," says Abergel. "It allows the internal membrane of the virus to fuse with that of the vacuole," she says.

Next, material from the virus spills out into the vacuole and turns it into a factory for making components of daughter virus particles. After a few hours, these assemble and mature into thousands of new pithoviruses which gather at the vacuole's edges before bursting out of a completely emaciated amoeba to find new host cells to infect. "It literally sucks the life out of the cell within 12 to 14 hours," says Abergel.

Unlike most viruses, including the pandoravirus, which hijack genes in the host nucleus to build new virus particles, the pithovirus uses its own
genes, proteins and enzymes to replicate. In this respect, it resembles the mimivirus, the first giant virus found by Claverie's team a decade ago.

Viral search

The team is now hunting for other viruses in the permafrost sample from the Kolyma region of northern Siberia. Claverie received the sample after contacting a team led by Elizaveta Rivkina of Russia's Institute of Physicochemical and Biological Problems of Soil Sciences in Pushchino, near Moscow. A year ago, Rivkina and her colleagues announced that they had revived a plant from the same layer of permafrost that eventually yielded the pithovirus.

Other permafrost researchers said the possibility that it harbours revivable viruses is real, and adds to the fear that reawakened microbes in thawing permafrost may increase global warming by digesting organic matter and releasing greenhouse gases such as methane and carbon dioxide.

"If on top of this we are now also seeing a possible release of potentially viable pathogenic viruses that are otherwise not living today, this will certainly add a whole further and new dimension to the thawing problem," says Torben Christensen of Lund University in Sweden. "It may mean that we are confronted not just with indirect climate warming impacts from thawing permafrost, but also direct human-health-related issues."

"Successful revival of any kind of ancient virus is always newsworthy," says Buford Price of the University of California at Berkeley. "My own group finds bacteria present at all depths in deep ice in the Antarctic and Greenland. The pithovirus is so large that we might be able to see it in ice cores more than 100,000 years old at their bases," he says.

But Janet Jansson of the Lawrence Berkeley Laboratory in California, who studies permafrost biodiversity, is more cautious about describing permafrost as a reservoir of potential pathogens. "Most of the microbes found in permafrost that we have studied are similar at the phylum level to microbes in most soils and some marine environments, so I don't think that permafrost per se should host more pathogens than any other environment," she says.

Claverie says that his team is also planning to hunt for large viruses in much older permafrost samples, from as early as 3 million years ago, to see if any can be revived.