A detailed new study of the origins of viruses lends weight to the argument that they are living cells, and offers us a reliable method to turn back the clock and track their evolution.
Viruses are just about everywhere. In us, on us, around us, at the depths of the ocean along scorching hot vents, even chilling out in the Siberian permafrost; and there are plenty to go around. This ubiquitous and abundant distribution is like what we see with bacteria. And again, much like bacteria, some are harmless, whereas others can do a lot of damage to their host, sometimes even killing them.
So at this point, to the untrained eye they may sound kind of similar. But there is one (of many) key difference that sets them apart: bacteria are living, and viruses are not. Well, that has been the opinion of many virologists, but there has been a long history of changed minds regarding what viruses are, and this debate is still very much alive.
So why are viruses so hard to classify? The main argument against their status as a living organism stems from the fact that viruses are completely dependent on hosts to replicate. Sure, viruses can survive outside of cells, but they can’t make any progeny. That’s because they don’t own the tools to be able to do so. More specifically, they can’t make proteins from their genetic material, which is why these slave drivers take over a cell and force it to do the dirty work.
That’s not really a clincher, though, as dependence on another organism for survival is not unique to viruses, and even some bacteria and fungi can’t go it solo. And then there are the recently discovered mimiviruses, which totally threw virologists. Viruses were always tiny simpletons with few genes, invisible to the light microscope. But these viruses are so big they were initially mistaken for bacteria, have genomes larger than some bacteria, and own some protein synthesis machinery.
Needless to say, the score is not settled, but scientists were hopeful that tracing their origins may offer some clues. That’s not easy when viruses don’t leave us fossils behind, and when we have only identified a few thousand of the millions predicted to exist. But where there is a will, there is a way. Researchers at the University of Illinois decided to follow their evolutionary breadcrumbs by examining the 3D shape and structure of proteins, or folds, which are written into the genome. That’s because viruses mutate all the time, but changes don’t necessarily affect the crucial folds which impart a particular function.
So they used computers to scrutinize folds of more than 5,000 organisms, almost 3,500 of which were viruses, covering every single branch of the tree of life. This led to the discovery of 442 protein folds that are common between viruses and cells, and 66 only found in viruses.
“This tells you that you can build a tree of life, because you’ve found a multitude of features in viruses that have all the properties that cells have,” lead researcher Gustavo Caetano-Anollés said in a statement. “Viruses also have unique components besides the components that are shared with cells.”
That last point is interesting, because it goes against the idea that viruses were merely bits of genetic material spat out by cellular life, or that they had stolen all of their genes from cells.
The researchers then built a tree of life that incorporated viruses, which revealed that modern viruses seem to have originated from multiple ancient cells, rather than modern cells, and even coexisted with the ancestors of today’s cells, they report in Science Advances.
“Viruses now merit a place in the tree of life,” said Caetano-Anollés. “Obviously, there is much more to viruses than we once thought.”
