Inside the Sprint to Map the Murder Hornet Genome

These days, if you stand in the right spot in Whatcom County, Washington, you can almost always catch a faint whiff of orange juice and rice wine. Scattered at regular intervals across the northwesternmost county of the contiguous United States, hundreds of large, plastic bottles filled with a few inches of the mixture hang from trees, oriented so their sweet, sticky perfume can catch any gentle breezes wafting through the wooded terrain. They’re not some weird pagan offering. They’re wasp traps. And they’re bigger than most traps you’ve probably seen before, because they’re designed to catch the world’s largest wasp, the Asian giant hornet. Or, as it’s more sensationally known on the interwebs: the “ murder hornet.”

This insect normally lives in the forest-draped mountains of eastern Asia. Then, late last year, it turned up in North America. Not that many, yet: Just one nest in British Columbia, and so far a few individual hornets discovered dead or caught in traps just across the border in Whatcom County have been confirmed. But the foreign insect’s arrival and subsequent media frenzy still led to hundreds of reports of other potential sightings as far afield as Florida (none of which have proved credible).

To be fair, the black-and-yellow-banded insect is alarmingly large for these parts—up to two inches long, enough to span an average adult’s palm. And its sting is among the most venomous in the world, delivered in large doses through its sizable stinger. One beekeeper who was stung seven times told The New York Times, “it was like having red-hot thumbtacks being driven into my flesh.” In Japan, the hornets kill up to 50 people each year.

Fatalities typically result from provocation. Asian giant hornets will defend their nest if it’s disturbed, but most of the time they’re not aggressive toward humans, or even interested in them. The behavior that earned them their bloodthirsty nickname is a feeding pattern they go through in the early fall, when they need to stock up on protein ahead of the breeding season. That’s when they switch from a diet of mostly oak tree sap and individual insects to something entomologists call “mass attacks.” They swarm on other groups of social insects, using their powerful mandibles to rip off their heads and eat the insides. In Japan, these frenzied feasts consist mostly of beetles. In North America, the Asian giant hornet appears to have found an easier target: domestic honey bees.

Honey bees and other native bees pollinate 75 percent of the fruits, nuts, and vegetables grown in the US. And they’re already declining in huge numbers due to habitat loss and pesticides. Native bees have no natural defenses against this invasive predator. Asian giant hornets can wipe out a whole beehive in a few hours, decapitating the adults before gobbling up the larvae and pupae.

So while overblown fears of a human-hunting hornet invasion were quickly dispelled months ago, and the country moved on to a cascade of real existential threats—like the Covid-19 pandemic, the federal government’s unconstitutional crackdown on anti-racism protests, and now, California’s raging wildfires—scientists and agricultural officials in the US and Canada have been racing to find, contain, and learn everything they can about the Asian giant hornets before they make a new home for themselves in the Pacific Northwest.

That includes assembling, for the first time, a complete map of the voracious insect’s genome.

After working furiously through the summer, researchers at the US Department of Agriculture released the hornet’s sequence to the public earlier this month. The major scientific milestone will be a boon for evolutionary biologists seeking to better understand the population dynamics of the species. As researchers continue to probe the genetic code, it may one day give up the toxic recipe for the hornet’s venomous sting, or offer clues about what chemicals or viruses might effectively bring it under control. But more urgently, it will help entomologists and pest managers track down where these early North American settlers came from and stop them from spreading.

“Sequencing the Asian giant hornet genome has been a real pushing-the-envelope sort of project for us,” says Anna Childers, a computational biologist with the USDA’s Agricultural Research Service, or ARS. Childers works in the agency’s Bee Research Lab in Beltsville, Maryland, and leads its genome assembly group. Since 2011, scientists at the agency have been sequencing agriculturally important arthropods—not just bees, but flies, ticks, beetles, and lots of other bugs, too—as part of the agency’s contribution to the “i5k” initiative, itself one arm within a planet-scale sequencing moon shot known as the Earth BioGenome Project.

I5k’s goal was to catalog the genomes of 5,000 species within five years. But as of yet, the sequences of only 78 organisms have been completed, according to the initiative’s database. Insect genomes, it turned out, proved particularly challenging to map. For one thing, their chitin-covered bodies are small, so there’s often not much genetic material to work with. That leads to more errors and patchier sequences. Complicating matters further, some bugs actually have molecules in their eyes that block the action of the enzymes that sequencing machines employ to build and read genes.

More recently, sequencing companies like Pacific Biosciences and Oxford Nanopore have developed newer technologies to surmount some of these challenges. In 2018, ARS decided to combine some of these new methods with the hard-earned insect sequencing expertise the agency had gained over the past few frustrating years into a new effort targeted at the bugs that pose the biggest threat to the nation’s crops, livestock, bees, and trees. The Ag100Pest Initiative, as it is known, originally aimed to provide reference-quality genome sequences for the worst 100 of these nuisance insects, though the tally has since grown to 134. ARS scientists published their first genome off the list last year—that of the spotted lanternfly, another invasive that has decimated vineyards and orchards in the Northeast US. Their next project is the desert locust, city-size swarms of which are right now causing a dual disaster of plagues in Africa.

Initially, the Asian giant hornet didn’t make the USDA’s list, because in 2018 no one had ever seen one in North America. Its native range extends west from northern India to Japan, and from Russia’s Far East heading south to Thailand and Vietnam. Even when the first North American specimen was discovered last summer in British Columbia, Childers says there wasn’t much appetite at the agency for trying to get a sample to sequence. “People thought it was probably just a stray,” she says. But then, in August, beekeepers in the town of Nanaimo, on Vancouver Island, came across three more, which led them to a nest. And before they destroyed it, they managed to collect samples—four dinner plate-sized combs containing developing hornets, 200 workers, and the queen.

By early September, five of those hornets, all workers, had made their way into the freezer at Leonard Foster’s lab at the University of British Columbia. Foster runs the university’s proteomics core, and he’s also, as he puts it, “nearly the only bee researcher in British Columbia.” He was holding onto the insects for safekeeping, in the unfortunate event that more nests were found. Then the DNA inside their frozen cells would become important for comparing the original Nanaimo discoveries against other sites of invasion—to track their spread across the continent through subtle differences in their genetics.

Over the winter, another hornet was photographed in White Rock, on mainland British Columbia. Two more were found near Blaine, Washington, about 10 miles away, across the Canada–US border. Reports of suspicious beehive massacres in the area also began to appear. The threat of a hornet invasion was looking more and more real. Childers’ team kicked into high gear to figure out what they could do to help. In April, they got lucky. Someone at the USDA put her in touch with Foster, a long-time agency collaborator. He agreed to send her one of his specimens.

From Canada, the specimen traveled on dry ice to Hilo, Hawaii, where USDA scientists extracted DNA from the insect’s thorax. Then they chopped up the genetic material and attached molecular tags to it, so a sequencer inside a USDA lab in Clay Center, Nebraska, would be able to read the pieces of its code. From there, digital files containing these pieces were uploaded to Ceres, the USDA’s supercomputer, so Childers’ team could use powerful genome assembly algorithms to stitch those pieces together. They worked on it throughout the summer, from their pandemic-mandated home offices. After two months, the sequence was finished, all 8.3 million letters.

The ARS team released the data to the public in early August. Typically, scientists wait to do this until they’ve mined a genome they’ve just assembled for all sorts of premier publication-worthy discoveries. But it was important to Childers that they get the sequence out as quickly as possible so that others could use it. “We were trying to make the process of genome sequencing part of a real-time response to an invasive species,” she says. “That would be a real paradigm shift.”

Although no one had ever before assembled a complete Asian giant hornet genome, researchers in China had previously sequenced bits and pieces—including the insect’s full mitochondrial DNA. That would prove useful to scientists at the Washington State Department of Agriculture. Earlier this year, before Childers got her hands on a hornet, WSDA entomologists snipped a leg off the first specimen found in the US—the one that had appeared one morning last December on a porch near Blaine. They shipped it to a lab in Japan to have its mitochondria sequenced. Then they convinced Canadian officials to do the same with one insect from the Nanaimo nest.

An initial genetic examination determined that the two North American specimens were not connected, as Telissa Wilson, a pest biologist with WDSA, told The New York Times in May. The American sample looked closer, genetically speaking, to a subspecies of the hornet that lives in South Korea. And the Canadian sample was a near-100 percent match for those found in Japan. But, Wilson told WIRED last week, additional analyses performed since then have complicated the picture.

That’s because the South Korean and Japanese subspecies have overlapping native ranges, but only a few specimens have ever been sequenced. So it’s possible that two individuals from different subspecies somehow got caught up and transported across the Pacific Ocean together. It’s perhaps not the most likely scenario, but it’s certainly possible. “The bottom line is we can’t say with certainty that these were two separate introductions,” Wilson says.

The only way to know for sure is to collect and sequence lots more hornets from across their native ranges, to get a better picture of their family tree and which branches are potential launching pads for a transoceanic journey. The aim of all this genetic detective work isn’t to lay blame on any particular trading partner, says Childers, though that information would certainly be useful for helping Customs and Border Patrol target specific shipments for inspection. That might help stop future introductions of pests. But knowing more about an invading hornet’s old home also provides clues about how to find its new one. “It’ll give us additional insights about how that animal behaves in its native range,” says Childers. “Which will help us better know how to target our efforts here.”

That endeavor will get a big boost now that researchers around the world have access to a full reference genome, says Todd Gilligan, a biological scientist in the USDA’s Animal and Plant Health Inspection Service. This year, APHIS organized a task force and dedicated $400,000 to support exotic hornet research and Washington state’s eradication efforts. “The complete Asian hornet genome sequence is the most important reference that we have regarding future molecular research on this species,” he wrote in a statement to WIRED.

It’s kind of like a numbered key to a puzzle, telling you where each piece goes. Subsequent sequences are much easier to assemble. APHIS and ARS are now working with several partners, including WSDA and university labs both here and abroad, to sequence more specimens. Because many of the specimens aren’t in great condition—sitting in traps for a long time degrades DNA—they expect to be able to sequence only smaller fragments. Before this data can be used, these fragments have to be lined up in the right locations. Without the complete genome sequence, this puzzle-fitting process would be a slogfest. But now, scientists can get answers much faster. And for people like Sven-Erik Spichinger, every minute counts.

As the managing entomologist for the Washington State Department of Agriculture, Spichinger has spent the past eight months conducting a statewide hornet hunt. Since the spring, his teams have set more than a thousand traps and have spent every day this summer managing them—changing out the orange juice/rice vinegar slurry once a week and checking for any victims. They got their first hit on July 14, an unmated queen captured near Birch Bay. Because she’d overwintered from the year before, this queen wouldn’t be able to start a new nest. But two weeks later, they trapped their second, a male, near Custer. “A male can only come from a nest that’s active this year,” says Spichinger.

Last week, a potential third was discovered—a worker, also near Birch Bay—but its species has yet to be confirmed in the laboratory, and the agency has not publicly announced its finding. The find, if validated, would suggest that there’s more than one nest in the area. Birch Bay and Custer are located about 5 kilometers apart. Since Asian giant hornets are capable of flying up to 8 kilometers, it’s possible there’s just one nest in the middle, says Spichinger. “But we have to treat it like they’re doing the typical thing and only straying one kilometer from their nest to forage,” he says.

That means setting more traps, but this time, a different kind—ones with a screen over the bait that ensnare the hornet without drowning it. If they can catch any hornets alive, they’ll fix a radio tag to their bodies and follow the signal back to their stronghold. Once they’ve got a location, they’ll use thermal imaging to pinpoint the nest, which buzzes with activity at around 85 degrees Fahrenheit. Only then will they send in exterminators in extra-thick bee suits to dig up the nest and eradicate its inhabitants.

Or, that’s the hope, anyway. So far, they haven’t trapped any live ones. “Right now we have a general idea of the wooded patches where a nest might be, but the area is still too large to walk up to it,” says Spichinger. Asian giant hornets dig their nests in the ground in rugged, wooded terrain. Most of those patches are surrounded by an impenetrable 10-foot buffer of thorny Himalayn blackberry bushes, says Spichinger. He’s not about to send people wielding chainsaws to chop them down when they might be right on top of a nest. “It’s one of the most dangerous activities we’ll do, so we want to have a few more data points before we go sending an army of people out there,” he says.

While they wait for the traps to work, Spichinger hopes that continued genetic sequencing will help narrow down the areas they have to search. Since hornets from different regions have different biological features and behaviors, their DNA can yield clues about what kinds of foods they prefer, what altitudes they tend to live in, and even how far from the nest they typically forage. “We can use that information to guide our response, including getting better baits,” he says. Since no one in North America makes Asian-giant-hornet-specific traps, they’re kind of winging it with the orange juice and rice vinegar. They’re also testing out other formulations and some chemical lures. Having more information about what these particular pioneers like to eat might help improve trap hit-rates.

That matters because the clock is ticking. Right now, the hornets are eating sap and any bugs they can find. Back in the nest, they’ll spit out that juice to feed the worker brood. But as daylight temperatures start to dip in the fall, the nests will switch over to producing drones and virgin queens. That’s when they’ll be on the hunt for honeybees.

In Japan, this happens sometime toward the end of September and early October. Spichinger doesn’t know exactly how their lifecycle will play out here, but he knows that if scientists don’t find the nests before then, the queens and drones will emerge and fly off to start their own nests. And that means the hunt will only get harder. Still, he’s optimistic that they’re getting close. Spichinger says there’s a good chance the Asian giant hornet can be prevented from establishing a permanent presence in the US. “It’s not a lost battle,” he says, “by any stretch of the imagination.”

Inside the Sprint to Map the Murder Hornet Genome

Author: sgadmin

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