Scientists Find Over 300 'Huge' Viruses With Strange Abilities

“Normal”-sized phages infecting a bacterial cell.
“Normal”-sized phages infecting a bacterial cell.
Image: Graham Beards (Wikimedia Commons (CC BY 3.0)

Scientists are continuing to discover weird-as-hell viruses all over the world. This week, researchers detailed their finding of relatively mammoth bacteriophages, viruses that infect bacteria. These large microorganisms don’t just dwarf typical viruses in size—they also seem capable of complex tricks normally only seen in living things.

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In recent years, we’ve become aware of all sorts of viruses much bigger than usual, some even larger than certain bacteria. It isn’t only physical size that makes these viruses big; it’s their genetics. The influenza A virus has eight genes, for instance, amounting to 13 thousand base pairs of DNA. But the largest viruses so far discovered have hundreds of genes, with more than a million base pairs, and can be visible under the weakest-powered microscopes.

These giant viruses, as they’ve come to be known, have largely been found in amoebas, often in environments far away from humans. But researchers have now found similarly large phages in places both more exotic and closer to home. Last year, a team documented large phages living inside the gut bacteria of people in Bangladesh. In a new study published today in Nature, that same team has now provided evidence of even larger phages living across the globe.

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Scientists nowadays often study and discover new viruses by sifting through the collective DNA soup of samples taken from the environment. In this case, the researchers looked at samples taken from human and animal poop, fresh and marine bodies of water, muddy sediments, and hot springs, among other environments. Then they screened out any microbes that likely weren’t phages, including other viruses. Finally, they tried to reconstruct the genomes of what was remaining.

“The genomes [we found] are large, some very much larger than ‘typical’ phages,” study author Jill Banfield, a professor of earth and planetary science at the University of California, Berkeley, told Gizmodo in an email.

Banfield and her team say they identified over 300 kinds of phages that were larger than 200,000 base pairs. The largest one they found was more than 735,000 base pairs—more than 10 times the genetic size of the average phage. These “huge phages,” as the team has dubbed them, also seemed to have genes normally found in living organisms and cells, genes that should let them pull off some pretty complex tricks.

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Many of the huge phages, for instance, have genes important to a system used by bacteria to fend off viruses, known as CRISPR. While most of us might think of CRISPR as a nifty gene-editing technology, its origins are an ancient immune system used by bacteria (as well as another single-celled branch of life, called archaea) to slice up the DNA of hostile viruses that want to infect them. These CRISPR-relevant genes, study author Basem Al-Shayeb told Gizmodo, might be used by huge phages to amplify the defenses of their hosts, in a form of “inter-viral warfare to target and destroy other viruses competing for the same host cell.”

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The new findings are only the latest to illustrate just how little we understand viruses. The lifelike abilities seen in large viruses muddle the picture of what a virus—typically seen as a non-living entity—really is. Even among large viruses, things aren’t so simple.

Huge phages, though similar in some aspects to other giant viruses, probably aren’t very closely related to them, much in the same way that bacteria aren’t closely related to amoebas or other eukaryotes (organisms whose cells have a distinct nucleus). Instead, the team argues, they belong to wholly different groupings, or clades, of viruses. Of the 350-plus huge phages they found, the team divided them into 10 separate clades, each given a name meaning “huge” in the native language of a co-author. The American clade? “Whopperphage.”

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While amoeba-loving giant viruses may not be a problem for people, the same might not be true for huge phages. Phages living in the human gut are known to influence the gut microbiome, which could affect people’s risk of certain diseases. They may also transfer genes to bacteria that can make them more antibiotic resistant or more likely to cause disease. Right now, though, research on the health effects of phages is limited. At the same time, scientists might be able to improve tools like CRISPR by studying these strange viruses.

What’s certainly true, Banfield said, is that the world of viruses—whether they infect amoebas, people, or bacteria—“is much more complicated and interesting than was previously believed.”

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Science writer at Gizmodo and pug aficionado elsewhere

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DISCUSSION

Giant virus? That’s not a giant virus. This is a giant virus.