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Virus-host relationships stretch back hundreds of millions of years

The viruses that today infect vertebrates, from fish to humans, have been evolving with their hosts for hundreds of millions of years, new research suggests.

A paper published in the journal Nature reveals a vast new trove of viruses – large in itself, but very likely a mere fraction of a yet undiscovered whole – found in almost 200 non-bird and non-mammal vertebrate species.

The research concentrates on the earliest form of virus to emerge – RNA viruses – and finds that although many cases of host-swapping can be found, the new data “reveals diverse virus-host associations across the entire evolutionary history of vertebrates”.

Vertebrates themselves – animals possessing a spinal cord – began evolving about 500 million years ago, and this work, led by Eddie Holmes of the Marie Bashir Institute for Infectious Diseases & Biosecurity at the University of Sydney, Australia, suggests that RNA viruses were there from the very start.

As other scientists have previously suggested, RNA viruses, because they emerged before DNA-based viruses, can be considered to pre-date the universal common ancestor that evolutionary theory tells us is at the base of Earth biology.

RNA viruses found in vertebrates, however, are more closely related to each other than they are to those adapted to invertebrates – a pattern that makes sense if vertebrate viruses themselves have all branched out from an initial type, in approximate lockstep with their hosts, since the phylum began.

In an accompanying opinion article in Nature, immunologists Mark Zeller and Kristian Anderson from the Scrips Research Institute in California, US, hail Holmes and colleagues for uncovering “astonishing biodiversity” among vertebrate RNA viruses – a diversity until now hidden because most research has focussed only on viruses that infect birds and mammals, ignoring the rest of the spinal cord world.

Holmes’s team sampled species chosen from amphibians, ray-finned fish and reptiles, and discovered 214 previously unknown types of virus. The number, write Zeller and Kristian, is probably a tiny fraction of the real virus population.

“Excluding birds and mammals, there are more than 50,000 vertebrate species,” they point out. “And although the current study is one of the largest of its kind, [the scientists] sampled less than 0.5% of these species.”

Also, they add, the sampling methods used by the researchers are designed to identify viruses that bear some level of genetic similarity to others already known. Therefore, it is possible that entire families, unknown by even a single example, remain to be discovered.

Despite the diversity, however, Zeller and Kristian, like Holmes and his colleagues, agree that RNA viruses in vertebrates share a common ancestry.

“The authors’ findings indicate that mammalian RNA viruses probably originated from viruses that infected fish, and then followed vertebrates on to land,” they write.

For his part, Holmes says the findings demonstrate that the virus “universe” is very large indeed.

“This study reveals some groups of virus have been in existence for the entire evolutionary history of the vertebrates – it transforms our understanding of virus evolution,” he says.

“For the first time, we can definitely show that RNA viruses are many millions of years old, and have been in existence since the first vertebrates existed. Fish, in particular, carry an amazing diversity of viruses, and virtually every type of virus family detected in mammals is now found in fish. We even found relatives of both Ebola and influenza viruses in fish.”