A recent paper in Science has announced the discovery of an organism that is going to require a reappraisal of our assumptions about viruses, evolution and the history of life. The authors named the organism Pandoravirus, in memory of the Greek myth about Pandora, who also unleashed something surprising with far-reaching consequences.
The publication by a group of French scientists describes a new kind of virus, which sounds like a little thing, but isn’t in this case for many reasons. The first reason is that these viruses are enormous. Not only are they bigger than Megavirus, the largest virus known, they contain more DNA and the genes they carry are sufficiently different from anything previously sequenced to qualify as a fundamentally new type of life.
We are literally going to have to rewrite the textbooks.
One aspect of this story that personally excites me is that of the two species described, one was found in a pond at my University. I am familiar with the ponds of La Trobe University in Melbourne, because I spent a year wading in them with a dip net collecting chironomids (a type of aquatic midge). This means that I have personally met the species Pandoravirus dulcis, at least biochemically. We just hadn’t been introduced until now.
Should I be worried about having contact with a really big virus? Does this mean I might get a big disease? No, because these viruses infect aquatic amoebas that live in muddy sediments. There is no evidence that they attack humans. Although, given how little we know about Pandoraviruses, we cannot rule out anything with confidence.
In an article about the discovery, a virologist is quoted as saying, “It’s like finding a sasquatch!” Except that it isn’t, because people have been actually looking for sasquatch, while until recently, nobody was looking for giant viruses.
These organisms were large enough to be seen using a light microscope, but unrecognised because everybody “knew” that you can’t see viruses with a microscope. They were hiding in plain sight.
Of course, it is impossible to tell if a cell is a virus just by looking at it. French scientists Jean-Michel Claverie, Chantal Abergel and their colleagues deserve credit for not only deciding to look for something that was considered more unlikely than a sasquatch, but for developing methods that allowed them to recognise what they had found.
In 2003, these scientists found a virus large enough to be seen by microscope. They named it Mimivirus, for “microbe mimicking virus”. It was so big it even had its own parasites, called virophages. Mimivirus also had far more genes than expected for a virus. As a comparison, the Aids virus has 10 genes and the influenza virus has 13; Mimivirus had up to 900 genes! For the first time it made sense to search for large viruses.
The French scientists began by inoculating Acanthamoeba with water samples collected from around the world and then watching for patterns of cell death that indicated a viral infection. In other words, when the amoebas began to explode, the scientists took a closer look. In 2011 they found a virus larger than any seen before and named it Megavirus.
Pandoravirus are massive at one micrometre: almost twice as big as Megavirus. The larger species, Pandoravirus salinus, was found at the mouth of a river in Chile, and the smaller species, P. dulcis, was found in Melbourne. This does not mean that these organisms are rare. Indeed, the discovery of two closely related organisms in distant locations suggests that they are probably quite common and have a worldwide distribution.
When the researchers examined the Pandoravirus DNA they found multiple surprises. Pandoravirus have far more genes than any other virus: up to 2556 protein coding sequences in P. salinas and 1502 genes in P. dulcis. Although they share 14 of the 31 genes usually found in large viruses, 93% of their genes resemble nothing known. (They even have introns!) And yet Pandoravirus still meet the criteria for being a virus: they do not have any genes for protein translation and they do not reproduce by binary fission.
In fact, the description of their reproductive cycle is fascinating. The particles disappear when they first enter the amoeba’s cell, but then thousands of viruses inside an envelope are assembled in a “a manner similar to knitting”. This is hard to explain, but imagine a bag full of potatoes where the potatoes are assembled along with the bag. I think this is extraordinary. Who knits potatoes?
These organisms will surely live up to their name, which the authors chose for “the surprises expected from their future study”. One of those surprises will be the ability to look at the evolution of viruses. Looking for large viruses is a way of looking back in time.
A virus is a cell without enough components to even be considered alive, technically. In some circles, at least, they are considered inert particles, more chemistry than biology. The typical virus contains only few genes and cannot reproduce without using the machinery of a host cell. There must have been a time when their ancestors had a full set of genes and lived independently. Pandoravirus is a window into that world.
It is also likely to lead to a reappraisal of the main branches of the tree of life. The three Domains (bacteria, archaea and eukaryotes) may soon become four. There are few discoveries that can claim to require such a substantial rethink about the nature of life.
And to think it came from some mud that I have literally washed from between my toes!