There’s a science story making the rounds this week that could easily pass as a plot for a low-budget science-fiction flick. A team of French scientists have awakened a giant virus that was encapsulated for 30,000 years in 100 feet (30 metres) of permafrost ice taken from coastal tundra in Chukotka, East Siberia. The most chilling (no pun intended) B-movieish aspect of this is that the huge (in this context meaning large enough to be seen under a microscope) ancient microbe is still infectious. Its host targets, fortunately, are amoebae, but other such reawakened viruses may not be as discriminating.
There is concern in the scientific community that resurrection of this long-dormant virus raises apprehension that other unknown pathogens entombed in frozen soil may be unleashed by climate change could pose potential risks for human health.
The discovery is described in a paper published in the journal Proceedings of the National Academy of Sciences (PNAS) entitled “Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology” (10.1073/pnas.1320670111), which notes that this pandoravirus-like particle may correspond to an unexplored diversity of unconventional DNA virus families, and that “The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health.”
British science writer Ed Yong, who authored a report on the discovery in Nature News this week, notes in his National Geographic Society “Not Exactly Rocket Science” blog that researching the story got him into a mini-debate about the magnitude of health risk such resurrected viruses may represent.
In his Nature News report (Nature dpi:10.1038/nature.2014.14801), Yong notes that the newly thawed virus is the biggest one ever found, being at 1.5 micrometres long, comparable in size to a small bacterium. The discovery was made by a team led by evolutionary biologists Jean-Michel Claverie a Professor of Medical Genomics and Bioinformatics at the University of Mediterranée School of Medicine, Director of the Mediterranean Institute of Microbiology, and head of the Structural and Genomic Information Laboratory, a CNRS unit (UPR2589) in Marseille, and his wife Dr. Chantal Abergel of the French national research agency Centre National de la Recherche Scientifique (CNRS) at Aix-Marseille University
AFP reports that the research team thawed the virus and watched it replicate in a culture in a petri dish, where it infected an amoeba (a simple single-celled organism). The team named the huge virus Pithovirus sibericum, inspired by the Greek word ‘pithos’ for the large container used by the ancient Greeks to store wine and food. P. sibericum has 500 genes, compared with the influenza virus that has only eight.
Drs. Claverie and Abergel have been in the hunt for what they and their colleagues call “pandoraviruses” because of their amphora shape and the surprises their discovery may portend — referencing the mythical Greek Pandora who opened a box and released evil into the world. Pandoraviruses are a genus of very large viruses, with genomes much larger than those of any other known type of virus, whose size approaches (and with this latest discovery surpasses) 1 micron in a blob-like shape resembling some types of bacteria.
Another paper published in the journal Science last summer (Science 19 July 2013: Vol. 341 no. 6143 pp. 281-286 DOI: 10.1126/science.1239181) entitled “Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes.” notes that:
“Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba, initiated a reappraisal of the upper limits of the viral world, both in terms of particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions typical of parasitic bacteria. The diversity of these giant viruses (the Megaviridae) was assessed by sampling a variety of aquatic environments and their associated sediments worldwide. We report the isolation of two giant viruses, one off the coast of central Chile, the other from a freshwater pond near Melbourne (Australia), without morphological or genomic resemblance to any previously defined virus families. Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the first members of the proposed “Pandoravirus” genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study.”
Dr. Claverie’s main research interest is the evolutionary origin and the biology of the paradoxical giant DNA viruses such as Mimivirus and the biodiversity of the marine microbial world (protists, bacteria and viruses). His laboratory’s approaches include structural, molecular, and cellular biology, high throughput genome and transcriptome sequencing, large-scale comparative genomics, and the development of relevant bioinformatic methods for sequence analysis and datamining. He also has a strong interest in the application of high throughput new generation sequencing genomic approaches in the biomedical and biotechnological fields. He is the co-author of more than 160 scientific publications in international journals and of the best-seller books “Bioinformatics for Dummies” and Bioinformatics For Dummies, 2nd Edition.
“The discovery of Pandoraviruses is an indication that our knowledge of Earth’s microbial biodiversity is still incomplete.” Dr. Claverie, told Inside Science News Service’s Ker last year. “Huge discoveries remain to be made at the most fundamental level that may change our present conception about the origin of life and its evolution.”
Discovered in the late 19th century, viruses have long been considered inert microbes, hardly qualified as living organisms and little more than a protein package of genetic material with no metabolic capabilities and incapable of replicating on their own, obliging them to parasitically invade and occupy cells and coax their host to replicate them, because they can’t make their own proteins. However, about a decade ago, discovery in an amoeba of a virus that rivals the size of a small bacterium prompted a rethinking of how viruses originated and what they could do. University of Mediterranée microbiologist Dr. Didier Raoult, Dr. Claverie, and colleagues sequenced the genome of mimivirus, for “microbe mimicking virus,” with 1.18 million bases contained more than 900 putative genes, some closely resembling genes in non-A class of their own. “These viruses have more than 2,000 new genes coding for proteins and enzymes that do unknown things, and participate in unknown metabolic pathways,” Dr. Abergel told ISNS’s Ker. “Elucidating their biochemical and regulatory functions might be of a tremendous interest for biotech and biomedical applications.”
On her CNRS Web page, Dr. Abergel notes that the researchers are now interested in genes conserved in large DNA viruses, and that analyzing them is a great opportunity to discover new “entry” points (molecular switches) in the control of cell death (apoptosis), cell division (DNA replication), or bacterial infection (phagocytosis, cell trafficking). This in turn might lead to innovative therapeutic approaches.
In his Science News report, Ed Yong cites Curtis Suttle, a virologist at the University of British Columbia in Vancouver, Canada, observing that: “Once again, this group has opened our eyes to the enormous diversity that exists in giant viruses.” Yong notes that two years ago, Drs. Claverie and Abergel’s team learned that scientists in Russia had resurrected an ancient plant from fruits buried in 30,000-year-old Siberian permafrost . “If it was possible to revive a plant, I wondered if it was possible to revive a virus,” comments Dr. Claverie. Using permafrost samples provided by the Russian team, the French scientists fished for giant viruses by using amoebae — the typical targets of these pathogens — as bait. The amoebae started dying, and the team found giant-virus particles inside them.
Back to the chilling part, Yong’s report notes that while giant viruses almost always target amoebae, Christelle Desnues, a virologist at the French National Centre for Scientific Research in Marseilles, last year discovered signs that another giant virus, Marseillevirus, had infected an 11-month-old boy who had been hospitalized with inflamed lymph nodes. Dr. Desnues’s team discovered traces of Marseillevirus DNA in the boy’s blood, and the virus itself in the a node. “It is clear that giant viruses cannot be seen as stand-alone freaks of nature,” she is quoted observing. “They constitute an integral part of the virosphere with implications in diversity, evolution and even human health.”
AFP cites France’s National Centre for Scientific Research (CNRS) saying in a press statement.
“[The resurrected virus discovery] has important implications for public-health risks in connection with exploiting mineral or energy resources in Arctic Circle regions that are becoming more and more accessible through global warming.
“The revival of viruses that are considered to have been eradicated, such as the smallpox virus, whose replication process is similar to that of Pithovirus, is no longer limited to science fiction.
“The risk that this scenario could happen in real life has to be viewed realistically.”
Yong reports that Drs. Claverie and Abergel are also concerned that rising global temperatures, along with mining and drilling operations in the Arctic, could thaw out and release many more ancient viruses that are still infectious and that could conceivably pose a threat to human health.
Metro News’s Mark Malloy cites Dr. Abergel saying the team are taking precautions to stop other viruses being released, noting “We are addressing this issue by sequencing the DNA that is present in those layers. This would be the best way to work out what is dangerous in there.”
Proceedings of the National Academy of Sciences (PNAS)
National Geographic Society
Inside Science News