As birds fly south for the winter, they're carrying with them some unwelcome cargo: the H5N1 virus, or bird flu.
In the past 30 days, the virus has struck 66 poultry flocks, leading to the deaths of more than 3.5 million turkeys, chickens and ducks, a steep increase compared to the summer months. The virus can spread easily when infected wild birds mix with commercial or backyard flocks.
At the moment, states in the middle of the country are hardest hit. But scientists expect more outbreaks in other parts of the country, given bird migratory patterns.
If not taken seriously, the fallout could lead to more than high egg prices. Influenza researchers fear a replay of last year when, for the first time, the U.S. saw close to 70 human cases, including one death.
"Absolutely we're going to see human infections, just like we did a year ago," says Seema Lakdawala, a virologist at Emory University who studies bird flu. "Nothing has changed substantially to suggest otherwise."
And though no human cases have been reported since early this year, scientists involved in tracking the virus say they don't have good visibility into what's happening in animals or humans. That's because the federal government has scaled back on surveillance and communication.
"We're not in a great position for monitoring things," says Wendy Puryear, a virologist at Tufts University. "I've been deep in the weeds since it arrived here in the U.S., and I'm finding myself in a very uncomfortable place."
Scaled back federal response
Puryear says a network of influenza researchers used to be in constant contact with their counterparts at federal health agencies about H5N1, mapping out research priorities and discussing changes in the virus.
But now, she says, "much of that infrastructure has been either completely closed down or significantly hampered," under the Trump administration, due to cutbacks in staffing, early retirements and other policies.
In fact, Puryear recalls a recent meeting that consisted entirely of her colleagues announcing they'd had to halt their studies related to H5N1 in humans because of the administration's funding cuts.
"It was a pretty depressing meeting," she says. "Just one person after another was closing their doors."
Another pressing issue: Data coming from the federally-run lab that does genetic sequencing of virus collected from infected animals has slowed to a trickle, something that was true even before the government shutdown, says Dr. Keith Poulsen, who runs the Wisconsin Veterinary Diagnostic Laboratory.
He says loss of staff at the U.S. Department of Agriculture — and the fact that communication with scientists needs to be "pre-approved" — has created obstacles, at a time when the threat of spillover from wildlife is increasing.
The shutdown has only exacerbated the situation.
For example, the network of veterinary labs that's responsible for testing ceased its regular meetings because of the shutdown, Poulsen says.
"The shutdown just kind of pours gas on a smoldering fire and makes us vulnerable," he says. "It's a national security issue."
USDA did not reply to a request for comment. In a statement, a spokesperson for the Department of Health and Human Services said the Centers for Disease Control and Prevention's influenza team was not affected by cutbacks and that response to urgent public health threats can continue during a shutdown.
A difficult virus to contain on farms
Based on reported data, cases in dairy herds appear to be relatively rare in recent months. A USDA program set up during the Biden administration to detect bird flu in dairy milk remains in place, as do rules that require cattle to be tested before they move across state lines.
But it's unclear how much routine testing is actually being done in cattle — and some like Lakdawala speculate the reported decline in cases could be due to a lack of testing.
The business model for dairy farms relies on moving cattle between farms, and new research from Lakdawala's team offers a sobering picture of why it's so hard to stamp out the virus on a farm.
They found it's pervasive — in the air of the milking parlor, all over the equipment, even in waste streams that sometimes get used to clean the housing facilities for the cattle.
Cows are "expelling it in their milk at such high levels," including animals that may have few or no symptoms, she says. "There is so much virus in the environment, these cows are bombarded with it. Of course, they're going to become infected."
As far as scientists can tell, the strain of H5N1 that's widely circulating has not seen the kind of mutations that would enable it to easily infect humans.
But Lakdawala says the conditions on farms with infected cattle are clearly a risk for workers who are essentially breathing in H5N1 particles that are aerosolized and remain infectious.
In Minnesota, which has seen about two dozen outbreaks on farms since mid-September, Karen Martin, an epidemiologist at that state's department of health, says they are monitoring about 35 people who were exposed in case they develop symptoms. The department is in contact with key people in the CDC's influenza division in case they need support.
"What concerns me is continuing to have the resources to respond to it. We're holding it together right now," she says.
A call for better testing of farm workers
Testing farm workers – the group at the highest risk of catching and spreading the virus – has been a problem since the beginning of the outbreak.
While some human cases have required hospitalization, most have been mild, often appearing as eye infections or other symptoms that are easily overlooked.
In a paper published last week, CDC scientists made a call for "robust data collection" of people with possible asymptomatic infections to better guide the public health response. One small study from last year found evidence of a past bird flu infection in 7% of dairy workers in Michigan and Colorado.
This kind of long-term research requires buy-in from farmers and their workers who are often undocumented. And that's unlikely to happen now because of fears about the Trump administration's immigration enforcement, says Bethany Boggess Alcaulter with the National Center for Farmworker Health.
"I think it's definitely more intense than it was, and already there was a lot of reluctance to get tested," she says.
When they were interviewing farm workers in California about bird flu this fall, she says many were too afraid to leave their homes. Their survey of several hundred workers in three states showed about 20% had symptoms at the same time animals on their farms were sick.
Most of those people said they were never tested.
Dr. Nirav Shah, who helped lead the bird flu response under President Biden, says it made sense for the CDC to downgrade its emergency response to bird flu earlier this year, but that should not have changed the work done to monitor the virus and respond on the ground.
"They are banking on the fact that there might not be anything, but that is a dangerous game to play when it comes to something like pandemic influenza," he says.
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