Aquatic viruses, algal-based biofuels
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Aquatic viruses, algal-based biofuels
Addressing the role of viruses in all aquatic systems.
Curated by David Dunigan
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Biogeography of Viruses in the Sea

Biogeography of Viruses in the Sea | Aquatic viruses, algal-based biofuels | Scoop.it

Viral ecology is a rapidly progressing area of research, as molecular methods have improved significantly for targeted research on specific populations and whole communities. To interpret and synthesize global viral diversity and distribution, it is feasible to assess whether macroecology concepts can apply to marine viruses. We review how viral and host life history and physical properties can influence viral distribution in light of biogeography and meta-community ecology paradigms. We highlight analytical approaches that can be applied to emerging global data sets and meta-analyses to identify individual taxa with global influence and drivers of emergent properties that influence microbial community structure by drawing on examples across the spectrum of viral taxa, from RNA to ssDNA and dsDNA viruses.

 


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Ed Rybicki's curator insight, September 9, 2015 10:57 AM

Excellent!  Just when we needed one B-)  Thanks, Flavia!

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Looking at protists as a source of pathogenic viruses

Looking at protists as a source of pathogenic viruses | Aquatic viruses, algal-based biofuels | Scoop.it

In the environment, protozoa are predators of bacteria and feed on them. The possibility that some protozoa could be a source of human pathogens is consistent with the discovery that free-living amoebae were the reservoir of Legionella pneumophila, the agent of Legionnaires' disease. Later, while searching for Legionella in the environment using amoeba co-culture, the first giant virus, Acanthamoeba polyphaga mimivirus, was discovered. Since then, many other giant viruses have been isolated, includingMarseilleviridae, Pithovirus sibericum, Cafeteria roenbergensis virus and Pandoravirus spp. The methods used to isolate all of these viruses are herein reviewed. By analogy to Legionella, it was originally suspected that these viruses could be human pathogens. After showing by indirect evidence, such as sero-epidemiologic studies, that it was possible for these viruses to be human pathogens, the recent isolation of some of these viruses (belonging to the Mimiviridae and Marseilleviridae families) in humans in the context of pathologic conditions shows that they are opportunistic human pathogens in some instances.

 

Mimivirus picture courtesy of Russell Kightley Media

  


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The unforeseen impact of densoviruses

The unforeseen impact of densoviruses | Aquatic viruses, algal-based biofuels | Scoop.it

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Ed Rybicki's curator insight, March 9, 2015 9:47 AM

I thank Flavia Flaviani for sending me this B-)

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New 'Intraterrestrial' Virus Found in Ocean Depths

New 'Intraterrestrial' Virus Found in Ocean Depths | Aquatic viruses, algal-based biofuels | Scoop.it

There are some pretty strange creatures found in the extreme temperature and pressure environment of the ocean bottom. But some of the weirdest are archaea, a primitive single-celled microorganism that scientists believe resemble the earliest life forms in the planet’s seas 3.5 billion years ago. Some archaea, which resemble bacteria but have a different genetic makeup, have developed the ability to eat methane and breathe sulfur or metal instead of oxygen — qualities that enable it to survive in deep ocean methane seeps on the sea floor, which would be inhospitable to most life forms.

 

But now, scientists from the University of California-Santa Barbara, supported by a National Science Foundation grant, have found something that’s even weirder. They’ve discovered a new virus that infects archaea, and in the process actually targets one of its own genes for mutation. Interestingly, the archaea itself has a similar ability to modify its genes.

  


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Zooplankton study could bridge gap between ecology and evolution

Zooplankton study could bridge gap between ecology and evolution | Aquatic viruses, algal-based biofuels | Scoop.it
UT Arlington biologist Matthew Walsh hopes to bridge the gap between ecology and evolution through his study of zooplankton in more than 20 lakes in Alaska and Wisconsin.

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How nature punches back at giant viruses

How nature punches back at giant viruses | Aquatic viruses, algal-based biofuels | Scoop.it
(Phys.org)—What have viruses ever done for humans? The question is debatable, but given the prevalence of highly contagious, and sometimes life-threatening illnesses caused by viruses, it's fair to say that most people would like to see the tables turned on these often-nasty bundles of DNA strands.

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Simple & elegant solution to a big problem in DNA based microbial diversity studies

Simple & elegant solution to a big problem in DNA based microbial diversity studies | Aquatic viruses, algal-based biofuels | Scoop.it
A new preprint has come out in PeerJ that presents a simple yet elegant solution to one of the bigger problems in DNA based microbial diversity studies.  The authors (Wenke Smets, Jonathan W Leff, ...

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Now curated by Mya Breitbart and Ed Rybicki:

If you would like to help curate it, please:

 

 contact: cupton at uvic dot ca


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Used contact lens solution hosts giant virus, ecosystem of parasites

Used contact lens solution hosts giant virus, ecosystem of parasites | Aquatic viruses, algal-based biofuels | Scoop.it

In July of last year, researchers in France described a rather disturbing example of what could happen if you're not careful about cleaning your contact lenses. A 17-year-old patient had been wearing monthly lenses well past their expiration date, and rinsing them with a cleaning solution she'd diluted with tap water. The end result was an eye infection...

 

Via @carlzimmer

 

Research article:

"Provirophages and transpovirons as the diverse mobilome of giant viruses"

http://dx.doi.org/10.1073/pnas.1208835109


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Towards defining the chloroviruses: [BMC Genomics. 2013]

Giant viruses in the genus Chlorovirus (family Phycodnaviridae ) infect eukaryotic green microalgae. The prototype member of the genus, Paramecium bursaria chlorella virus 1, was sequenced more than 15 years ago, and to date there are only 6 fully sequenced chloroviruses in public databases. Presented here are the draft genome sequences of 35 additional chloroviruses collected across the globe; they infect one of three different green algal species. These new data allowed us to analyze the genomic landscape of 41 chloroviruses, which revealed some remarkable features about these viruses.


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Ed Rybicki's curator insight, March 21, 2013 3:54 AM
I remember visiting James van Etten in Lincoln, Nebraska, just after his group had characterised PBCV-1: that was in 1982, and that virus was BIIIG news, in an environment where very few viruses had been sequenced at all, and definitely nothing as large as a chlorovirus. Strange that so few have been sequenced - but that will definitely change now.
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Genomes of Giant Viruses Hint at "4th Domain" of Life: Scientific American

Genomes of Giant Viruses Hint at "4th Domain" of Life: Scientific American | Aquatic viruses, algal-based biofuels | Scoop.it
Just 7 percent of the viruses' genes match those in existing databases, a finding that confirms that viral diversity is still largely underexplored
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A virus in a virus in a virus: Giant virus in an amoeba has a virophage which itself hosts transpovirons

A virus in a virus in a virus: Giant virus in an amoeba has a virophage which itself hosts transpovirons | Aquatic viruses, algal-based biofuels | Scoop.it

A team of researchers working out of the Centre National de la Recherche Scientifique in France has discovered a new giant virus living in an amoeba found in an eye patient's contact lens fluid. They also found a new kind of virophage inside the virus which itself was harboring a previously unknown class of genetic parasite they've named transpovirons.

 

The researchers named the giant virus Lentille and found that it belongs to a group of giant viruses known as Mimiviridae. They named the virophage – a virus that infects other viruses – living inside the Lentille virus, Sputnik 2, (Russian for "fellow traveler"). Inside of the virophage they found fragments of DNA that didn't belong to the amoeba, the giant virus or the virophage, indicating that it was class of unknown genetic parasite that they've named transpovirons.

 

Sputnik 2 is just the fourth known virophage and is unique in that it can insert its DNA into its host genome, which might explain why the genomes of different giant viruses are so similar. In looking closer at the virophage Sputnik 2, the team found fragments of DNA inside of it that didn't belong to any of the hosts; strands that outnumbered the giant viruses DNA by up to 14 times. Because there was no record of such fragments being observed before, the team gave them a name: transpovirons. As the name implies, the fragments were found able to jump in and out of host DNA in similar fashion to transposons.

 

The researchers believe transpovirons need giant viruses to replicate and are exceptionally good at reproducing and also appear to ride around in virophages. And because of the large variety of DNA found in them, the team believes they get their material from many different sources, similar in that respect to virophages, which other researchers have found contain the genomes of other giant viruses. Because only a small amount of work has been focused on giant viruses, the team believes it's likely that other virophages and transposons will soon be discovered as more resources are dedicated to their study.


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Giant Pandoravirus is 1,000 times larger than influenca virus and contains 2556 genes

Giant Pandoravirus is 1,000 times larger than influenca virus and contains 2556 genes | Aquatic viruses, algal-based biofuels | Scoop.it

Giant viruses turn out to be everywhere. It was the very giant-ness of giant viruses that allowed them to be overlooked for so long. Scientists first discovered viruses in the late 1800s when they were puzzled by a disease that beset tobacco plants. They mashed up wilted tobacco leaves with water and passed the mixture through fine porcelain filters that trapped bacteria and fungi. The clear liquid could still make healthy tobacco leaves sick. The Dutch botanist Martinus Beijerinck dubbed it “a contagious living fluid.”

 

In the 1930s, the invention of powerful microscopes finally allowed scientists to see viruses. They found that viruses were unlike ordinary cells: they didn’t generate their own fuel; they didn’t grow or divide. Instead, viruses invaded cells, hijacking their biochemistry to make new copies of themselves. Being small and simple seemed like part of the viral way of life, allowing them to replicate fast.

 

It wasn’t until 2003 that a team of French researchers discovered the first giant virus. They had been puzzling over sphere-shaped objects that were the size of bacteria but contained no bacterial DNA. Eventually they realized that they were looking at a monstrously oversized virus, containing 979 genes, much less than the newly discovered Pandoravirus.

 

Those first giant viruses were isolated from amoebae living in water from a cooling tower. Once scientists realized that viruses could be so large, they changed their search parameters and started finding other species in all manner of places, from swamps to rivers to contact lens fluid.

 

And along the way the biggest viruses got bigger. In 2011, Dr. Claverie and his colleagues set a new record with megaviruses, a type of giant virus with 1,120 genes they discovered in sea water off the coast of Chile. They then dug into the sediment below that sea water and discovered pandoravirsues, with more than twice as many genes.

 

Dr. Claverie speculates that pandoraviruses and other giant viruses evolved from free-living microbes that branched off from other life several billion years ago. “The type of cells they may have evolved from may have disappeared,” he said.

 

The idea that giant viruses represent separate branches on the tree of life is a controversial one that many other experts aren’t ready to embrace. “They provide no evidence for that notion, so it seems a distraction to me,” said T. Martin Embley, a professor of evolutionary molecular biology at Newcastle University.

 

Despite those reservations, Dr. Embley and other researchers hail pandoraviruses as an important discovery. “I think it’s wonderful that such crazy and divergent lifeforms continue to be discovered,” said Tom Williams, Dr. Embley’s colleague at Newcastle University.

 

The new study also drives home the fact that giant viruses are far from rare. Shortly after discovering pandoraviruses in sea floor sediment, Dr. Claverie and his colleagues found them in water from a lake in Australia, 10,000 miles away. “It definitely indicates that they must not be rare at all,” said Dr. Claverie.

 

Giant viruses may be so common, in fact, that they may be hiding inside of us, too. In a paper published online on July 2 in The Journal of Infectious Diseases, French researchers offered evidence that giant viruses dwell in healthy people. They isolated a new giant virus from blood donated by a healthy volunteer, and then found antibodies and other signs of the virus in four other donors.

 

Giant viruses may lurk harmlessly in our bodies, invading the amoebae we harbor. Whether they can make us sick is an open question. “I don’t believe we have the proof at the moment that these viruses could infect humans,” said Dr. Claverie.


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Tomas Moravec's comment, July 23, 2013 4:14 AM
It is surprising how these large gyus avoided discovery for such a long time.
Ed Rybicki's comment, July 23, 2013 4:17 AM
Well, if they look like bacteria, and we are still finding new exemplars of those...
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Study shows algal virus can infiltrate mammalian cells

Study shows algal virus can infiltrate mammalian cells | Aquatic viruses, algal-based biofuels | Scoop.it
New research led by the University of Nebraska-Lincoln has provided the first direct evidence that an algae-infecting virus can invade and potentially replicate within some mammalian cells.

Known as Acanthocystis turfacea chlorella virus 1, or ATCV-1, the pathogen is among a class of chloroviruses long believed to take up residence only in green algae. That thinking changed with a 2014 study from Johns Hopkins University and UNL that found gene sequences resembling those of ATCV-1 in throat swabs of human participants.

The new study, published in the Journal of Virology, introduced ATCV-1 to macrophage cells that serve critical functions in the immune responses of mice, humans and other mammals. By tagging the virus with fluorescent dye and assembling three-dimensional images of mouse cells, the authors determined that ATCV-1 successfully infiltrated them.


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Ed Rybicki's curator insight, October 21, 2015 1:08 PM

Right up there with evidence that mimiviruses may be implicated in pneumonia - we are nowhere near determining how many viruses are actually involved in human disease.

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An inexpensive, accurate and precise wet-mount method for enumerating aquatic viruses

Viruses affect biogeochemical cycling, microbial mortality, gene flow, and metabolic functions in diverse environments through infection and lysis of microorganisms. Fundamental to quantitatively investigating these roles is the determination of viral abundance in both field and laboratory samples. One current, widely-used method to accomplish this in aquatic samples is the ‘filter-mount’ method in which samples are filtered onto costly 0.02 μm-pore-size ceramic filters for enumeration of viruses with epifluorescence microscopy. Here we describe a cost-effective (ca. 500-fold lower materials cost) alternative virus enumeration method in which fluorescently-stained samples are wet-mounted directly onto slides, after optional chemical flocculation of viruses in samples with viral concentrations <5×107 mL-1. The concentration of viruses in the sample is then determined from the ratio of viruses to a known concentration of added microsphere beads via epifluorescence microscopy. Virus concentrations obtained using this wet-mount method, with and without chemical flocculation, were significantly correlated with, and had equivalent precision to, those from the filter-mount method across concentrations ranging from 2.17×106 to 1.37×108 viruses mL-1 when tested using cultivated viral isolates and natural samples from marine and freshwater environments. In summary, the wet-mount method is significantly less expensive than the filter-mount method, and is appropriate for rapid, precise and accurate enumeration of aquatic viruses over a wide range of viral concentrations (≥1×106 viruses mL-1) encountered in field and laboratory samples.

 


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Life in a phage world

Life in a phage world | Aquatic viruses, algal-based biofuels | Scoop.it

To celebrate a century of phage exploration, we invite you to get intimate with 30 diverse phages in this premier phage field guide. In these 404 pages you'll learn who these phages are, where on Earth they've been found, who their close relatives are, how their genomes are structured, and how they trick their hosts into submission. Researchers who have devoted their lives to phage also recount their experiences in pursuit of their quarry.

 


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Ed Rybicki's curator insight, February 27, 2015 5:36 AM

WHAT a good idea - in our continuing celebration of The Centenary of the Phage.  Thanks Zwirko!

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Biodiversity and distribution of polar freshwater DNA viruses

Biodiversity and distribution of polar freshwater DNA viruses | Aquatic viruses, algal-based biofuels | Scoop.it

Viruses constitute the most abundant biological entities and a large reservoir of genetic diversity on Earth. Despite the recent surge in their study, our knowledge on their actual biodiversity and distribution remains sparse. We report the first metagenomic analysis of Arctic freshwater viral DNA communities and a comparative analysis with other freshwater environments. Arctic viromes are dominated by unknown and single-stranded DNA viruses with no close relatives in the database. These unique viral DNA communities mostly relate to each other and present some minor genetic overlap with other environments studied, including an Arctic Ocean virome. Despite common environmental conditions in polar ecosystems, the Arctic and Antarctic DNA viromes differ at the fine-grain genetic level while sharing a similar taxonomic composition. The study uncovers some viral lineages with a bipolar distribution, suggesting a global dispersal capacity for viruses, and seemingly indicates that viruses do not follow the latitudinal diversity gradient known for macroorganisms. Our study sheds light into the global biogeography and connectivity of viral communities.

 


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Exclusive cross-domain networks in the sea

Exclusive cross-domain networks in the sea | Aquatic viruses, algal-based biofuels | Scoop.it
The identification of an exchange of nutrients and signalling molecules between a planktonic alga and a bacterium demonstrates that targeted mutualistic interactions occur across domains of life in the oceans.

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Ed Rybicki's curator insight, June 1, 2015 8:10 AM

All life is one B-)

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Massive Toxic Algae Blooms May Prove a Sign of Climate Change to Come

Massive Toxic Algae Blooms May Prove a Sign of Climate Change to Come | Aquatic viruses, algal-based biofuels | Scoop.it
The blooms off the U.S. West Coast may become more frequent

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How nature punches back at giant viruses

How nature punches back at giant viruses | Aquatic viruses, algal-based biofuels | Scoop.it
(Phys.org)—What have viruses ever done for humans? The question is debatable, but given the prevalence of highly contagious, and sometimes life-threatening illnesses caused by viruses, it's fair to say that most people would like to see the tables turned on these often-nasty bundles of DNA strands.

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Study of giant viruses shakes up tree of life | Science Wire | EarthSky

Study of giant viruses shakes up tree of life | Science Wire | EarthSky | Aquatic viruses, algal-based biofuels | Scoop.it
A new study of giant viruses supports the idea that viruses are ancient living organisms and not inanimate molecular remnants run amok, as some scientists have argued.

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Provirophages and transpovirons as the diverse mobilome of giant viruses

A distinct class of infectious agents, the virophages that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements, the transpovirons.


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Evidence of the megavirome in humans. [J Clin Virol. 2013] -

We serendipitously detected Mimivirus- and Marseillevirus-like sequences while using a new metagenomic approach targeting bacterial DNA that subsequently led to the isolation of a new member of the family Marseilleviridae, named Senegalvirus, from human stools. This discovery demonstrates the possibility of the presence of giant viruses of amoebae in humans. In addition, we detected sequences related to Megavirales members in several human metagenomes, which adds to previous findings by several groups.


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Chad Smithson's comment, June 3, 2013 5:52 PM
QQQQQ````````````1`11`1`111``1234`12343356787690 ==///**-/9==7789666-++++65411120002023...
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Giant Mimivirus - Link between non-living viruses and living organisms or just an anomaly?

Giant Mimivirus - Link between non-living viruses and living organisms or just an anomaly? | Aquatic viruses, algal-based biofuels | Scoop.it

 

Viruses are small and fairly simple. At least that's what many people probably assume. With the discovery of Mimivirus — the largest, most complex virus currently known — these assumptions may need to be reevaluated. This giant virus has a much larger size and bigger genome than any other known virus. Analysis of this intriguing virus may shed light on basic questions of viral evolution and, perhaps, the origins of life.

 

When most people think about viruses, they probably first think about diseases. Flu, polio, AIDS. We all know that viruses have caused immeasurable suffering throughout human history. And when asked to describe a virus, most people probably would say, "small." Indeed, viruses were first identified as filterable infectious agents — entities that could cause an infection and pass through a filter small enough to exclude almost all bacteria.

 

Their small size and inability to carry out translation — the formation of polypeptides from messenger RNA — often are highlighted as two defining characteristics of viruses. They seem to share little else. Some viruses have RNA genomes, and some have DNA genomes. Some have single-stranded genomes, and others have double-stranded genomes. Some possess envelopes, while others do not. And structurally, viruses display a wonderful array of shapes. The discovery of the giant Mimivirus certainly forces us to rethink our assumption that viruses are small. Analysis of this virus also may cause us to rethink our assumptions about the tree of life.

 

First observed in 1992, Acanthamoeba polyphaga mimivirus (APMV) presents an interesting story of scientific inquiry. During the investigation of a pneumonia outbreak, researchers noticed particles resembling Gram-positive bacteria residing within amoebae isolated from a water-cooling tower. Because other bacterial species that cause pneumonia, like Legionella pneumophila, reside within amoebae, the investigators hypothesized that they had found another pneumonia-causing bacterium. Subsequent research, however, showed that they had identified not a bacterium, but a giant virus.

 

Indeed, the most dramatic feature of this virus is its size. Researchers, in fact, named it Mimivirus — short for "mimicking microbe" — to reflect its large size and apparent Gram-staining properties. The virus has a capsid diameter of 400–500 nanometers (nm) and a total particle diameter, including fibers extending out from the capsid, of approximately 750 nm. A second strain of APMV, currently referred to as "mamavirus," may be even larger. These APMV strains dwarf all other known viruses and exceed the size of several well-characterized bacteria. Poliovirus particles, in comparison, have a diameter of only 30 nm, which is roughly 10,000 times smaller than a grain of salt. Even the relatively large, brick-shaped poxviruses, such as smallpox virus, usually measure about 200 nm wide and 300 nm long — not even half the size of Mimivirus. At approximately 1.2 million base pairs, the linear, double-stranded DNA genome of Mimivirus far exceeds the size of any other known virus and a number of bacteria. Again, as a point of comparison, poliovirus has a genome of only 7,500 nucleotides, and the smallpox virus genome is about 200,000 nucleotides long. While the size of Mimivirus certainly stretches our common perceptions of viruses, researchers have been more interested in the types of genes found within the Mimivirus genome. This information, they reasoned, could help us understand the evolutionary history of Mimivirus and, perhaps, shed some light on the more basic question of the history of all viruses. To carry out this type of analysis, genes within the Mimivirus genome would need to be compared to genes of other organisms. When organisms share similar genes, we can hypothesize that they share an evolutionary heritage.

 

Continue reading: http://tinyurl.com/2crc6vj


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Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

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.

 

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes
Nadège Philippe et al.

Science 19 July 2013:
Vol. 341 no. 6143 pp. 281-286
http://dx.doi.org/10.1126/science.1239181


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