TWiV 261: Giants among viruses

December 1, 2013

RingbergHosts: Vincent Racaniello and James Van Etten

Guests: Chantal Abergel and Jean-Michel Claverie

Vincent meets up with Chantal and Jean-Michel at the first International Symposium on Giant Virus Biology in Tegernsee, Germany, to discuss their work on Mimivirus, Megavirus, and Pandoravirus.

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  • Artem Baydaluk

    Is it necessary to make a survey of giant viruses in different parts of the world? and also, what approach is better to use: metagenomics – searching for similarity with already known giant viruses, different from others or trying to find new ones in the bottom samples and protists by using microscopy?

  • http://www.virology.ws profvrr

    If you asked the meeting participants they would say that we need to look all over the world, because you never know what you might miss by looking only in one area. That’s a lot of space but I don’t know how else to make sure we get a good sampling. I suspect that metagenomic analyses would be the method of choice, but not just by looking for similarity to known giant viruses – remember, Pandoravirus is barely similar to anything. You have to exclude what sequences we do know and look at the rest. But perhaps someone from the giant virus meeting will chime in here and give a good answer.

  • Artem Baydaluk

    Thank you. That’s so interesting groundbreaking topic. And nobody wants to start studying it in my country. It seems that researchers may not completely comprehend the reasons to study it in the rest of the world. Personally I think the data about how these giant viruses are distributed throughout the world (phylogenetic analyses linked with geografical positions) may be supporting to understand their evolution and covolution with the hosts. Furthermore, new questions may be elicited from such data. Or the direction of my thoughts is wrong? I try to find some advantages or disadvantages of such kind of survey.

  • Joseph Coco

    So if viruses have no ‘desire’ to regain functionality they have shed and learned to hijack something else’s, does this mean Mimiviruses are in a transition phase of minimizing their genome? Or are they keeping the functionality they currently have because there’s less selective pressure that way? I’m sorry if I missed this in discussion.

  • Matthias Fischer

    This is indeed one hypothesis about giant virus evolution and there is some experimental evidence that the genome termini of Mimiviruses are prone to rearrangements, including large deletions. See TWiV 139 for the full story. However, it is difficult to generalize, as giant viruses seem to inhabit a diverse range of environments, which influences the kind of selective pressure a given virus population will experience. Hence different genes will be important to reproduce in different environments.

  • Matthias Fischer

    Both approaches are important and I wouldn’t call one “better” than the other. It really depends on the question you’re asking. If you want to find relatives of known genomes, metagenomics will give you tons of useful data. But as Vincent said, this will not help you with the large percentage of unknown sequences that dominate metagenomic surveys. We need to have at least one representative for each major type of virus in culture, so we can link the genome data to a host and other information about the virus (virion structure, infection cycle etc.). And this is not just true for genes that are exclusive to giant viruses and have no recognizable homologs in cells.
    Take the DNA repair gene MutS for example. Before the Mimivirus genome was sequenced, any MutS homolog from a Mimiviruses found in metagenomic datasets would have been classified as coming from a bacterium or a marine invertebrate. Now we know that giant DNA viruses have their own distinct version of MutS, which can even be used as a marker gene to identify giant viruses (see Ogata et al, ISME J 5:1143-51, 2011).

    Isolation and metagenomics complement each other. Laboratory isolation of new viruses is cumbersome and involves a great deal of luck, but once you have a new virus in culture, you can characterize it in detail and then search for relatives in metagenomic databases.
    Metagenomics is high-throughput and will give you millions of gene sequences from a certain environment, but without cultured representatives you won’t be able to interpret the data.