NORTH GRAFTON — Just before 11 a.m. on a recent Thursday, Dr. Maureen Murray reached into a small cardboard box to pull out her next patient. She removed layers of a soft, leopard-patterned blanket and revealed the tiny face of a baby possum. A local wildlife rehabilitation center had called Murray’s team earlier that morning to report a small cut on its upper back.
The animal looked around the fluorescently lit intake room of the Tufts Wildlife Clinic, then opened its mouth as veterinarians swabbed the inside of its cheek.
That swab, along with ones from an injured turkey and a Cooper’s hawk with a damaged wing — all brought in that same morning by outside collaborators who work with wildlife — was then whisked across campus to the lab of virologist Jonathan Runstadler. His team at Tufts’ Cummings School of Veterinary Medicine would test the swabs for the deadly strain of bird flu that has led to the deaths of tens of millions of birds and infected dozens of mammal species around the world, including dairy cows.
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The lab, which tests animal samples from across the country, offers a peek at how scientists are racing to learn more about the virus, which experts are concerned may one day evolve to more easily infect people.
“It’s still very much an open question, scientifically: What’s going to happen as this virus continues to evolve and spread through animal populations?” Runstadler said.
On Thursday, Michigan state officials confirmed the third human case of H5N1 in the US this year, in a farm worker exposed to infected cows. The worker had respiratory symptoms, a first for humans exposed to infected cattle, and is recovering.
Officials around the country are on high alert for new cases. Last month, the CDC asked state and local public health officials to keep flu monitoring efforts high throughout the summer to quickly detect any uptick in human illness. The agency also launched a dashboard that tracks Influenza A viruses — H5N1 is part of that virus family — in wastewater samples from across the country to pinpoint transmission hotspots.
Runstadler’s work is an important piece of this broader monitoring effort. The lab tests a wide range of animals in hopes of catching H5N1 cases that might otherwise go undetected. One of their concerns is that the virus might make its way into an animal host that doesn’t show any symptoms. There, the virus could develop more worrisome mutations, such as those that may promote adaptation to mammals.
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“Those are the places where viruses can evolve and circulate, because nobody had an eye on the ball,” said Wendy Puryear, a virologist in Runstadler’s lab.
Bird flu isn’t new for Runstadler and his team. He formed his lab two decades ago to study flu viruses in animals. In 2013, the group began monitoring seals and, in the summer of 2022, became the first to identify and investigate the deaths of more than 180 gray and harbor seals from H5N1 off the coast of Maine.
The seal deaths concerned scientists because they were among the first signs that this strain of H5N1 could devastate mammals. Since then, the virus has killed tens of thousands of sea lions and seals in South America, and, more recently was detected in more than 60 dairy herds in nine states.
The lab is part of a network of Centers of Excellence for Influenza Research and Response, funded by the National Institutes of Health. It’s one of less than a dozen network members that conduct wildlife surveillance and even fewer that conduct sampling as broad as Tufts, said Puryear.
The question that members of the Runstadler lab are now asking is whether any new wild birds and mammals are being infected along the East Coast and across the country. The team has tested around 10,000 bird and 2,500 mammal samples — 1,000 of which are from marine mammals — since the virus hit the United States in 2022.
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The lab routinely finds positive H5N1 cases in birds, though they haven’t identified any mammals who have contracted the virus since the seal deaths in the summer of 2022. The USDA, however, has confirmed bird flu cases in over 200 mammals across the country including foxes, mountain lions, raccoons, and bears. The Runstadler lab has not tested any cattle, a process that is largely being handled by state and federal agencies, Puryear said.
In April, Runstadler traveled to a beach in Swampscott to swab a beached humpback whale. Though the large mammal tested negative for H5N1, whales have been shown to contract other types of influenza.
Bird samples are shipped to the lab from collaborators in New England and from as far south as Virginia. Samples from marine mammals come from Maine as well as Florida, California, Alaska, and even Hawaii. Lab members prepare care packages that include swabs, personal protective equipment, shipping materials, and instructions to help collaborators collect samples safely. Swabs arrive at the lab in small screw-cap tubes with a pink-colored liquid that helps preserve the samples. The tubes are placed inside Ziploc bags and packed in ice.
When a sample tests positive for H5N1, Puryear and her colleagues notify the submitter to warn them about potential contact with infected animals. They then send the sample to a USDA lab for confirmation. Either the Runstadler lab or a lab at the Icahn School of Medicine at Mount Sinai in New York City then sequences the RNA, or genetic information, of the virus to see if there are any changes in its code. A computer identifies abnormalities — like an “A” in the genetic code changing to a “C” — and the string of letters is uploaded to an online database. There, scientists across the world can access the sequences to pin down if and how the virus might be evolving.
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One concerning mutation, which makes the H5N1 virus better at copying itself inside of mammal cells, was detected in a seal the Runstadler lab tested in the summer of 2022. The mutation, called PB2 E627K, has also emerged in multiple mammals who contracted H5N1 in recent years and, in a paper published in the New England Journal of Medicine earlier in May, scientists reported the human who contracted H5N1 in Texas had also acquired the PB2 E627K mutation.
While that mutation is on scientists’ radars, they stress the virus would need additional genetic changes to promote spread between humans. In early April, the CDC said the presence of the mutation in the Texas farm worker did not change their assessment that the current risk of H5N1 to human health is low.
“I think one of the things that’s very valuable about their work is that it’s been continuous over time,” said Ana Silvia Gonzalez-Reiche, a virologist at Mount Sinai who collaborates with the Runstadler lab. “Throughout the years, they have accumulated a lot of data, and the value of that is that you can start seeing patterns and learning.”
Puryear and her colleagues don’t always know what samples they’re going to get in the mail on any given day. Around 11 a.m. on a recent Wednesday, a delivery man entered with the day’s packages. Puryear grabbed one — a cardboard box branded with a pet food logo that had been repurposed to transport animal samples — and placed it on the fridge’s bottom shelf.
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The next day, the team tested the box’s contents. One of the samples, belonging to a crow from Cape Cod, came back positive for H5N1.