Over 30,000 Virus “Stowaways” Discovered Hiding In Microbe Genomes

The impressive feat of detective work has revealed thousands of sequences that have never been seen before.

DNA sequences from over 30,000 previously unknown viruses have been discovered, thanks to a seriously powerful computer and some clever detective work. The team, led by Dr Christopher Bellas at the University of Innsbruck, was astounded when their study of a group of complex micro-organisms called protists came up with a whole lot more than they bargained for.

Genetic material left behind by viruses pops up surprisingly often in the genomes of lots of species, including humans. Called endogenous viral elements (EVEs), these are often characterized as viral “fossils” – they’re considered to be non-functional, mere relics of ancient viral infections. They certainly don’t appear to cause any harm to their host organisms, despite how very widespread they are.

“We were very surprised by how many viruses we found through this analysis,” said Bellas in a statement. “In some cases, up to 10% of a microbe's DNA turned out to consist of hidden viruses.”

Protists, the focus of this study, are single-celled, complex organisms that can happily live across many different environments on Earth, from oceans and lakes, to soil, and even inside other animals. Like other living things, protists are constantly subjected to viral infections. Some of these can be deadly; others might quietly insert themselves into the organism’s genetic code and then don’t appear to do very much of anything.

"Why so many viruses are found in the genomes of microbes is not yet clear," explained Bellas, but the researchers do have a theory: it could be that EVEs, far from being non-functional as many assume, are actually playing a protective role against other, more dangerous foes.

Protists are at risk from the suitably intimidating-sounding giant viruses, which can be as large as bacteria and are fatal to the organisms they infect. But there is some good news: the protists have a white knight in the form of virophages. Just as bacteriophages are viruses that kill bacteria, virophages are viruses that neutralize other viruses.

If a giant virus comes along and infects an organism that already has a resident virophage, the virophage will hijack the molecular machinery of the giant virus and cause it to create lots more virophage copies. This protects the original host cell from any damage by the giant virus and can save a population from destruction.

Bellas and the team noted that the tens of thousands of previously unknown EVEs they discovered seemed to have some similarities with virophage sequences, which is why they speculate that they may be having a protective effect.

The fact that so many new EVEs were discovered is an incredible achievement in itself. The study authors originally went hunting for the origins of a very specific group of viruses called Polinton-like viruses, which Bellas and a colleague discovered in the waters of an Austrian lake back in 2021. In order to do this, however, they needed to cast the net wide.

“We did not know which organisms are usually infected by these viruses. That's why we conducted a large-scale study to test all microbes whose DNA sequences are known," Bellas explained.

What resulted was a huge amount of DNA sequence data. Working through it all would be a daunting task, so the researchers enlisted the help of a super-powerful computer cluster called Leo, as well as some state-of-the-art lab techniques. They could never have hoped to find as many as 30,000 new EVEs, and future research can now focus more deeply on the potential roles they play. We might find that they’re not just “fossils” after all.

The study is published in Proceedings of the National Academy of Sciences.

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