Pithovirus: Bigger than Pandoravirus with a smaller genome

4 March 2014

PithovirusA new virus called Pithovirus sibericum has been isolated from 30,000 year old Siberian permafrost. It is the oldest DNA virus of eukaryotes ever isolated, showing that viruses can retain infectivity in nature for very long periods of time.

Pithovirus was isolated by inoculating cultures of the amoeba Acanthamoeba castellani with samples taken in the year 2000 from 30 meters below the surface of a late Pleistocene sediment in the Kolyma lowland region. This amoeba had been previously used to propagate other giant viruses, such as Mimivirus and Pandoravirus. Light microscopy of the cultures revealed the presence of ovoid particles which were subsequently shown by electron microscopy to resemble those of Pandoravirus. Pithovirus particles are flask-shaped and slightly larger than Pandoravirus – 1.5 microns long, 500 nm in diameter, encased by a 60 nm thick membrane. One end of the virus particle appears to be sealed with what the authors call a cork (photo). This feature, along with the shape of the virus particle,  inspired the authors to name the new isolate Pithovirus, from the Greek word pithos which refers to the amphora given to Pandora. The name therefore refers both to the morphology of the virus particle and its similarity to Pandoravirus.

Although the Pithovirus particle is larger than Pandoravirus, the viral genome – which is a double-stranded molecule of DNA – is smaller, a ‘mere 610,033 base pairs’, to use the authors’ words (the Pandoravirus genome is 2.8 million base pairs in length). There are other viruses with genomes of this size packed into much smaller particles – so why is the Pithovirus particle so large? Might it have recently lost a good deal of its genome and the particle size has not yet caught up? One theory of the origin of viruses is that they originated from cells and then lost genes on their way to becoming parasitic.

We now know of viruses from two different families that have similar morphology: an amphora-like shape, an apex, and a thick electron-dense tegument covered by a lipid membrane enclosing an internal compartment. This finding should not be surprising: similar viral architectures are known to span families. The icosahedral architecture for building a particle, for example, can be found in highly diverse viral families. The question is how many viruses are built with the pithovirus/pandoravirus structure. My guess would be many, and they could contain either DNA genomes. We just need to look for them, a process, as the authors say that ‘will remain a challenging and serendipitous process’.

Despite the physical similarity with Pandoravirus, the Pithovirus genome sequence reveals that it is barely related to that virus, but more closely resembles members of the Marseillviridae, Megaviridae, and Iridoviridae. These families all contain large icosahedral viruses with DNA genomes.  Only 32% of the 467 predicted Pithovirus proteins have homologs in protein databases (this number was 61% for Mimivirus and 16% for Pandoravirus). In contrast to other giant DNA viruses, the genome of Pithovirus does not encode any component of the protein synthesis machinery. However the viral genome does encode the complete machinery needed to produce mRNAs. These proteins are present in the purified Pithovirus particle. Pithovirus therefore undergoes its entire replication cycle in the cytoplasm, much like other large DNA viruses such as poxviruses.

Pithovirus is an amazing virus that hints about the yet undiscovered viral diversity that awaits discovery. Its preservation in a permafrost layer suggests that these regions might harbor a vast array of infectious organisms that could be released as these regions thaw or are subjected to exploration for mineral and oil recovery. A detailed analysis of the microbes present in these regions is clearly needed, both by the culture technique used in this paper and by metagenomic analysis, to assess whether any constitute a threat to animals.

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  • Rich

    Interesting to think about “life-like” entities that can be trapped in time, and then released at a later date. It could represent another life-cycle that we have not yet become fully aware of since the cyclic nature of polar glaciations spans many many human lifetimes. Maybe it could develop into a new field, viro-glaciology!

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  • Brigitte

    Amazing!

  • spock

    Amazing!
    This could be the incipit of a SiFi movie. “The giant-virus came back from 30k yy sleep in the antarctic permafrost. And it is not alone” (as V. Racaniello clearly stated in the last paragraph). As a molecular biologist I’d pay (well no… let’s say I can work for free :-) ) to be part of the research team involved in digging out these bugs from the past and study them and their ancient ecological niche.

  • http://www.virology.ws profvrr

    Really interesting point. Microbes could be frozen for long periods of time then releases, skipping a great deal of evolution. How about glaciovirology?

  • http://www.virology.ws profvrr

    It is such a cool story, and it’s particularly great that they actually isolated the virus by culturing.

  • http://www.virology.ws profvrr

    I suspect that the authors obtained the Siberian sample as doing the coring is very expensive. So you just have to have a lab, and get samples from the right places. I’m sorry to say that doing this kind of work, at least in the US, will be difficult because funding for exploration is hard to come by. Sadly.

  • Zwirko

    Maybe the particle is so large so as to ensure that the amoeba “sees” the virus? Assuming, that is, that the virus gains entry through phagocytosis…

  • http://www.virology.ws profvrr

    Large particle size could be partly a consequence of facilitating uptake by the host. However, we don’t know the actual host for the virus in nature. It could be amoeba, could be something else.

  • spock

    well, here in Italy, this kind of work is mostly done by teams directly funded by the CNR (National Council of Research). Indeed many of them are “lucky” enough to reside in one of the few italian permanent structures based in the Antarctica. Well, I am not one of them (ranked just second in a national competition and now in my forties). Sadly, few months ago one of this brave young scientists died while diving in a mission to collect biological specimen. Love for science and a life-commitment for the reserch can, sometimes, be a sort of curse. :-(

  • DMLopez

    This is incredible! This is the Ozti of viruses!! I can’t wait for what it has to tell us.

    I wonder if a “naked” virus lacking a cell-derived membrane would withstand such conditions and remain infectious after thawing.

  • http://www.virology.ws profvrr

    It would probably would be best to look for an icosahedral phage, by infecting bacteria known to be in these areas with the permafrost material. I bet they are infectious – icosahedral capsids can be very stable.

  • Bruna

    Well, I think we’re just uncovering some nice guys! The only thing I can say is that the virome we know is nothing compared to what really exists.

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  • RMichel

    Nobody recognized in this article on the recent detection of the giant Pithovirus sibiricum that intracellular microorganisms observed within acanthamoebae from surface water exhibited an identical morphology described as early as 1998 and 2003 in Germany. As cited by Legendre et al.(2014) the strain isolated previously was called „KC5/2„ and had an oval crossstriped wall and an apical opening or pore comparable to that described with Pithovirus. Intense genomic investigations are going on in order to compare the genetic makeup with that of Pithovirus. The details of KC5/2 were described only recently: Michel et al (2013) Journal of Endocytobiosis and Cell Research 24: 12-15

  • Jalish Mahmud Riyad

    To me, the most significant finding is that due to climate change and global warming, many unknown pathogens can come out of their dormant state. We already know that bacteria can survive in harsh conditions such as the arctic. Think about the implication of this research in this angle. Many pathogens that MIGHT have attacked other Homo species in prehistoric time can come back to life again, who knows. Also, accidentally, some of the virus/ other pathogens might find humans a suitable host. Since there are more than 7 billion people on planet, there is ample opportunity for a pathogen to go through trial and error.

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  • http://archive.org/details/antifederalist_0707_librivox The Federal Farmer

    due to climate change and global warming