Ancient Viruses Hiding in Plain Sight

By: TAMU Biology

One lazy Saturday morning, coronavirus researcher Dr. Ben Neuman of Texas A&M University’s Biology Department decided to fire off a quick online search for corona-like viruses, as he had done so many times before. This time though, he baited his search with a distant relative of coronaviruses called Aplysia abyssovirus. The results were astounding – over a dozen new, deeply weird virus genomes that had been lying, apparently unrecognized, in datasets from spiders, centipedes and plankton animals.

Across the globe, Dr. Chris Lauber of Twincore in Hannover, Germany set out with similar goals, and two new programs he had written to comb a giant database called the Sequence Read Archive for fragments to assemble into new viruses. The two teamed up to hunt viruses together, and the result was 76 of the strangest viruses ever seen, published this week in the prestigious Proceedings of the National Academy of Sciences, USA (www.pnas.org/doi/10.1073/pnas.2413675122)

Other members of the team tested small parts of the new viruses and found that they could tell cells to pause or slide backward one step while making protein, avoiding stop signals. The researchers think the new viruses use these signals to chain together assembly lines of components to do complex tasks.

Viruses that cause diseases like the flu are essentially self-copying genetic code, and each group of viruses usually has one or two ways of doing that, called replication modes. But among the new viruses of sea anemones, earthworms, leeches and snails they found evidence for 8 distinct replication modes. Dr. Neuman said, “We’re going to be studying these new viruses for a long time, and we have a lot to learn.”

The evolutionary implications were enormous. Here was a long line of viruses packed with potentially powerful genes so strange that we can only imagine what they do – the entire coronavirus ancestry laid bare. “When you find a new virus, it’s like getting your DNA ancestry – all of a sudden, you are surrounded by a world of second and third cousins and bits of Neanderthal that you didn’t know before. Then imagine that feeling 75 more times. It’s not a new family tree, it’s a forest.” said Dr. Neuman.

The group intends to study the new viruses, and has already started unearthing more. “Wait until you see what’s coming next,” said Dr. Neuman. “This is a real game-changer, but it’s only the beginning.”