A fruit fly stuck to a dowel, thanks to the parasitic fungus inside it. Carolyn Elya

The story of the misplaced virus—a discovery that Michael Eisen describes as one of the wackiest of his career—began with some plates of fruit.

In the summer of 2015, Carolyn Elya, a member of Eisen’s team at the University of California, Berkeley, began leaving fruit out in her backyard, in a deliberate attempt to attract flies. Predictably, the insects arrived. Unpredictably, some of them died in a strange way. When Elya found their bodies, their wings were erect, and a fungus was sprouting through their backs. She recognized the fungus as Entomophthora muscae, a species whose name aptly means “destroyer of insects.” It kills flies. And before it does that, it controls them.

When an Entomophthora spore lands on a fly, it grows into the insect’s body and begins devouring it alive, consuming the fat first and leaving vital organs till last. When the fly is nearly spent, the fungus compels it to do three things. First, it climbs to a high point. Next, it extends its mouth as if to lap up some food, but becomes stuck to its perch thanks to a glue that the fungus produces. Finally, it lifts its wings like a fancy sports car raising its doors. This is how the fly dies: innards consumed, face stuck, and wings out of the way.

The fungus now pushes long tubes through the back of its dead host. Each tube is a cannon, which shoots out fungal spores at up to 21 miles per hour. The spores rain down on other passing flies, and new cycles of death and puppeteering begin.

The natural world is full of such mind-controlling parasites that subvert the behavior of hosts. The rabies virus makes its hosts more aggressive, the cordyceps fungus turns ants into zombies, and the Toxoplasma parasite sends rats scurrying toward the scent of cats. Even microbes like Entomophthora, which lack brains and bodies of their own, can commandeer the nervous systems of more complex animals.

Eisen thinks there are countless other examples that we have yet to discover. “Microbes are the most innovative part of life,” he says. “Logic tells us that any time there are interactions between microbes and animals, which is all the time, some microbes will have figured out ways of manipulating the behavior of their host to their advantage.”

Fascinating though these puppeteers are, they’ve traditionally been hard to study because they and their hosts are hard to rear in laboratories. For that reason, Eisen has spent years searching for parasitic microbes that manipulate the fruit fly Drosophila—a mainstay of lab research. If successful, he could use all the slickest tools of neuroscience and genetics to work out exactly how the parasite works its mojo.

But most leads fizzled out. Eisen’s team tried to see if the yeast the flies eat could influence their actions. Nope. They checked if the microbes in their guts had an effect. Nada. That, ironically, was why Elya started leaving plates of fruit out. She wanted to collect wild Drosophila to check if their gut microbes differed substantially from the lab-bred insects. But when she discovered the Entomophthora-riddled carcasses, it seemed that she had inadvertently found the puppeteer that Eisen had been searching for.

Entomophthora was discovered back in 1855, but scientists had almost always found it in houseflies—a group that diverged from fruit flies back in the Cretaceous period. Elya became the first researcher to successfully get the fungus to infect lab-reared Drosophila, which allowed her and her colleagues to study it in earnest.

They began sequencing the fungus’s RNA—the molecule that’s produced when its genes are switched on. To their surprise, they found that around 10 percent of these sequences matched a virus, which had been discovered just three years ago. A team of British researchers had found its RNA among wild Drosophila, which they had collected from the English village of Twyford. “I thought, that can’t be a coincidence,” says Eisen. “We’re working on a fungus that infects Drosophila and here’s a virus from Drosophila.”

At first, Eisen didn’t even believe that the Twyford virus was actually a virus at all. Many viruses can insert their genes into those of their hosts and stay there permanently; around 8 percent of the human genome consists of domesticated viruses like these. Similarly, Eisen suspected Twyford was a former virus that had become part of the fungus’s genome. And the fungus, with those viral genes in tow, had gotten into the flies that the British team captured. Cute story, he thought, and promptly forgot about it.

But months later, the team completed sequencing the fungus’s genome. And when Eisen couldn’t find any traces of viral genes within the fungal sequences, he realized he’d been wrong. Twyford really was a bona fide virus. His student Maxwell Coyle even managed to isolate it, view it through a microscope, and confirm that it infects the fungus.

The virus, which the team have renamed Entomophthovirus, is part of an obscure family called the iflaviruses. (“I hadn’t heard of them, and I used to be a virologist,” Eisen says.) Almost all the known iflaviruses infect insects. But Entomophthovirus is different: It infects a fungus that infects insects. That’s a considerable change, since insects and fungi belong to two very different kingdoms of life that have been separated by a billion-plus years of evolution.

It’s not clear how the virus initially made this massive cross-kingdom leap, but it is clearly at home in its new host. Coyle and Eisen found that the virus and the fungus are almost always found together, whether in a Californian yard or an English village. Whenever the team detected the virus’s genes in a fly, the fungus was invariably there, too. And whenever they found the fungus, they also found the virus. The pair “are moving around from fly to fly in what we think is a perfect association,” Eisen says. “And that means one of two things.”

It’s possible that the virus is just so good at infection that the fungus can’t get rid of it. But Eisen thinks that’s unlikely. Under lab conditions, his team and others have managed to isolate fungal spores that don’t carry any Entomophthovirus inside them.

The more interesting alternative is that the virus is responsible for the fungus’s mind-controlling powers. “Maybe the fungus can lose the virus, but when it does, it no longer affects fly behavior and is unsuccessful as a parasite,” Eisen says. That’s still a hypothesis, but a very tantalizing one, especially when considering what other iflaviruses can do. One of them seems to make honeybees more aggressive. Another is injected into ladybugs by parasitic wasps, and seems to turn the ladybugs into docile bodyguards for the wasps’ eggs. Entomophthovirus comes from a family of puppeteers. Maybe it is also one itself.

“It’s a really exciting idea, but there is no experimental evidence just yet,” says Brittany Leigh from Vanderbilt University. “Still so much is unknown about the viruses of fungi, let alone their ability to interact with insects.”

“We’re still waiting for the killer experiments, which we’re doing,” Eisen says. His colleagues are checking if the fungus can still control the flies after it has been cleared of the virus. They want to see if the fungus releases chemicals that could influence the flies, and if it does so only when the virus is present. They’re even trying to inject the virus directly into flies to see what happens. These tests would all support the idea that the virus is the key to the fungus’s manipulative abilities.

It’s also possible, says Nolwenn Dheilly from Stony Brook University, “that the virus could be a parasite within a parasite.” Perhaps instead of helping the fungus, it harms it, or keeps it in check? Eisen likes that idea, too. “It could be a complicated relationship where the virus is making the fungus sick, but is also imbuing it with an ability to transmit its own infection,” he says. “Then how do you classify it?”

Dheilly suspects that these complicated relationships are more commonplace than we think. “Many viruses that have been described so far may not infect the host that has been assigned to them, but a parasite infecting the host,” she says. She is now launching a new project to try and find these parasites of parasites, and work out how they influence the lives of the creatures that carry them.

The poet Jonathan Swift would have approved. As he wrote in 1733:

The vermin only teaze and pinch
Their foes superior by an inch.
So, naturalists observe, a flea
Has smaller fleas that on him prey;
And these have smaller still to bite ‘em,
And so proceed ad infinitum.
Thus every poet, in his kind,
Is bit by him that comes behind.

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