Giant viruses shake up the status quo

A quick microbiology primer before we begin, for the uninitiated or those who don’t have a 14 year old in their lives to ask.

Microbe is a catch-all terms that we use to describe microscopic organisms. These may or may not be pathogenic (disease-causing). They include, but are not limited to:

  • Bacteria (like E. coli and S. aureus, which cause food poisoning)
  • Fungi (like athlete’s foot and brewer’s yeast)
  • Protists (like Plasmodium, which causes malaria and Naegleria, which you might have seen in an episode of House)

We probably shouldn’t include viruses (like the common cold) or prions (like variant CJD) in there because they’re not really classified as organisms: they’re not alive, simply inert particles that harness other living things to replicate themselves. As my year 8s would tell you, they don’t do MRS NERG (movement, reproduction, sensitivity, nutrition, excretion, respiration or growth). 

It’s a question of scale

Microbes and … non-microbes? vary widely in size, but as a general rule viruses are pretty tiny and pretty simple. HIV is just 100-150nm across. Bacteria are usually considerably bigger (a virus can infect a bacteria and make many thousands of copies inside). E. coli is 2 microns across. Protists are single-celled eukaryotes, like amoeba, large enough to predate bacteria in many case. Plasmodium is around 5x bigger than E. coli  Fungi vary hugely in size, from yeasts to mushrooms with underground networks covering an entire field, but are generally also at the large end.

We generally expect the size of the genome to correlate with the size of the microbe: viruses tend to have genomes <1Mb (1 million bases), while free-living bacteria range from around 2-12 Mb. Protists are in the region of 10Mb or more, but can have a smaller genome when they are obligate parasites.

A change in the status quo

So far, so good. But ten years ago, a French group discovered the first giant virus, which was so large it was originally mis-identified as a parasitic bacterium. For the first time, a virus had been found that could be seen under a light microscope and had a genome of more than 1Mb. Since then, many of these Mimiviruses (from microbe mimicking virus) have been identified, including the largest known so far Megavirus chilensis. Interestingly the mimiviruses have many genes that we’re not used to seeing in viruses, suggesting that it had descended from a free-living cell that gradually lost genes, in the way we see in mitochondria and chloroplasts according to endosymbiotic theory. This suggests that somewhere out there there could be an even bigger virus, that had lost slightly fewer of its genes.

Curiouser and curiouser

M. chilensis was discovered infecting Acanthamoeba: so a French group set out to search for new giant viruses where they knew that these amoeba thrived, in an Australian pond and coastal sediments from Chile. By pinpointing samples where the amoeba were disintegrating, they found a new particle that was replicating inside the ameoba. These were even bigger than the previously recognised Megaviridae, being 1 micron by 0.5 microns, but they had a very different appearance. It was later found that they didn’t have key capsid-producing proteins, so the virus lacked the coat seen in the mimiviruses. They didn’t respond to antibiotics though, suggesting that they were not bacterial. By observing the replication cycle of the parasites, where one particle produced thousands more, rather than just two as we see in binary fission, this was confirmed and the new viruses were named Pandoravirus salinus and Pandoravirus dulcis.

A Pandora’s box of giant viruses

The genomes of both viruses were sequenced and estimated to be around 2.47 and 1.91 megabases each. This contained 2556 putative protein-coding genes in P. salinus and 1502 in P. dulcis. These genes didn’t include those necessary for energy production, meaning that the parasites can be confirmed as being viruses. By comparing the two genomes it was shown that they show great similarity to one another, although P. salinus contains four large genomic segments not seen in the other virus. Weirdly though, very few of these genes had any relationship with genes seen in other organisms. The pandoraviruses seem to be from a completely different ballpark altogether.

So why the name? As the original article says “[the name reflects] their lack of similarity with previously described microorganisams and the surprises expected from their future study.” Is it just me, or is Pandora a bit of a pessimistic thing to be calling them?! Fingers crossed it’s only a reference to the number of new viruses we expect, and we won’t be in need of a special Hopevirus!

_______________________________________________________Philippe, Legendre, Doutre, et al. (July 2013).
“Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes”
Science 341 (6143): 281–286

La Scola, Audic, Robert, et a (2003).
“A giant virus in amoebae”
Science 299 (5615): 2033

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