For decades, environmental and farm groups pushed Congress, the USDA and farmers to adopt new conservation programs, but progress came in incremental steps. With each Farm Bill, some lawmakers threaten to whittle down conservation programs, but they have essentially managed to survive and even expand.
The country’s largest farm lobby, the American Farm Bureau Federation, had long denied the realities of climate change, fighting against climate action and adopting official policy positions that question the scientific consensus that climate change is human-caused. Its members—the bulk of American farmers—largely adhered to the same mindset.
But as the realities of climate change have started to hit American farmers on the ground in the form of more extreme weather, and as funding opportunities have expanded through conservation and climate-focused programs, that mindset has started to shift.
“They were concerned about what climate policy meant for their operations,” Bonnie said. “They felt judged. But we said: Let’s partner up.”
The Trump administration’s rollbacks and freezes threaten to stall or undo that progress, advocacy groups and former USDA employees say.
“We created this enormous infrastructure. We’ve solved huge problems,” Bonnie added, “and they’re undermining all of it.”
“It took so long,” Stillerman said. “The idea that climate change was happening and that farmers could be part of the solution, and could build more resilient farming and food systems against that threat—the IRA really put dollars behind that. All of that is at risk now.”
Burk says he plans to continue with conservation and carbon-storing practices on his Michigan farm, even without conservation dollars from the USDA.
But, he says, many of his neighboring farmers likely will stop conservation measures without the certainty of government support.
“So many people are struggling, just trying to figure out how to pay their bills, to get the fuel to run their tractors, to plant,” he said. “The last thing they want to be doing is sitting down with someone from NRCS who says, ‘If I do these things, maybe I’ll get paid in a year.’ That’s not going to happen.”
Over the weekend, the Trump administration fired several frontline responders to the ongoing H5N1 bird flu outbreak—then quickly backpedaled, rescinding those terminations and attempting to reinstate the critical staff.
The termination letters went out to employees at the US Department of Agriculture, one of the agencies leading the federal response to the outbreak that continues to plague US dairy farms and ravage poultry operations, affecting over 160 million birds and sending egg prices soaring. As the virus continues to spread, infectious disease experts fear it could evolve to spread among humans and cause more severe disease. So far, the Centers for Disease Control and Prevention has documented 68 cases in humans, one of which was fatal.
Prior to Trump taking office, health experts had criticized the country’s response to H5N1 for lack of transparency at times, sluggishness, inadequate testing, and its inability to halt transmission among dairy farms, which was once considered containable. To date, 972 herds across 17 states have been infected since last March, including 36 herds in the last 30 days.
In a statement to Ars Technica, a USDA spokesperson said that the agency views the response to the outbreak of H5N1—a highly pathogenic avian influenza (HPAI)—as a priority. As such, the agency had protected some positions from staff cuts by granting exemptions, which went to veterinarians, animal health technicians, and others. But not all were exempted, and some were fired.
“Although several positions supporting HPAI were notified of their terminations over the weekend, we are working to swiftly rectify the situation and rescind those letters,” the spokesperson said.
The USDA did not respond to Ars Technica’s questions regarding how many employees working on the outbreak were fired, how many of those terminations were rescinded, or how many employees have been reinstated since the weekend.
The cuts are part of a larger, brutal effort by the Trump administration to slash federal agencies, and the cuts have imperiled other critical government and public services. In recent days, several agencies, including the National Institutes of Health, the CDC, the National Science Foundation, and the Department of Energy, among others, have been gutted. At CDC, cuts devastated the agency’s premier disease detectives program—the Epidemic Intelligence Service—members of which are critical to responding to outbreaks and other health emergencies.
However, the new Nevada case is notable because it marks the first time D1.1 is known to have jumped from birds to cows to a person. Moreover, D1.1 has proven dangerous. The genotype is behind the country’s only severe and ultimately fatal case of H5N1 so far in the outbreak. The death in the Louisiana case linked to wild and backyard birds was reported last month. The CDC’s statement added that the person had “prolonged, unprotected” exposure to the birds. The D1.1. genotype was also behind a severe H5N1 infection that put a Canadian teenager in intensive care late last year.
In a February 7 analysis, the USDA reported finding that the D1.1 strain infecting cows in Nevada has a notable mutation known to help the bird-adapted virus replicate in mammals more efficiently (PB2 D701N). To date, this mutation has not been seen in D1.1 strains spreading in wild birds nor has it been seen in the B3.13 genotype circulating in dairy cows. However, it was seen before in a 2023 human case in Chile. The CDC said it has confirmed that the strain of D1.1 infecting the person in Nevada also contains the PB2 D701N mutation.
The USDA and CDC both reported that no other concerning mutations were found, including one that has been consistently identified in the B3.13 strain in cows. The CDC said it does not expect any changes to how the virus will interact with human immune responses or to antivirals.
Most importantly, to date, there has been no evidence of human-to-human transmission, which would mark a dangerous turn for the virus’s ability to spark an outbreak. For all these reasons, the CDC considers the risk to the public low, though people with exposure to poultry, dairy cows, and birds are at higher risk and should take precautions.
The spread of H5N1 bird flu in dairy cows is unprecedented; the US outbreak is the first of its kind in cows. Virologists and infectious disease experts fear that the continued spread of the virus in domestic mammals like cows, which have close interactions with people, will provide the virus countless opportunities to spill over and adapt to humans.
So far, the US has tallied 67 human cases of H5N1 since the start of 2024. Of those, 40 have been in dairy workers, while 23 were in poultry workers, one was the Louisiana case who had contact with wild and backyard birds, and three were cases that had no clear exposure.
Whether the D1.1 genotype will pose a yet greater risk for dairy workers remains unclear for now. Generally, H5N1 infections in humans have been rare but dangerous. According to data collected by the World Health Organization, 954 H5N1 human cases have been documented globally since 2003. Of those, 464 were fatal, for a fatality rate among documented cases of 49 percent. But, so far, nearly all of the human infections in the US have been relatively mild, and experts don’t know why. There are various possible factors, including transmission route, past immunity of workers, use of antivirals, or something about the B3.13 genotype specifically.
For now, the USDA says that the detection of the D1.1 genotype in cows doesn’t change their eradication strategy. It further touted the finding as a “testament to the strength of our National Milk Testing Strategy.”
Enlarge/ A recall notice is posted next to Boar’s Head meats that are displayed at a Safeway store on July 31, 2024, in San Rafael, California.
The Boar’s Head deli-meat plant at the epicenter of a nationwide Listeria outbreak that killed nine people so far harbored the deadly germ in a common area of the facility deemed “low risk” for Listeria. Further, it had no written plans to prevent cross-contamination of the dangerous bacteria to other products and areas. That’s according to a federal document newly released by Boar’s Head.
On Friday, the company announced that it is indefinitely closing that Jarratt, Virginia-based plant and will never again produce liverwurst—the product that Maryland health investigators first identified as the source of the outbreak strain of Listeria monocytogenes. The finding led to the recall of more than 7 million pounds of Boar’s Head meat. The Jarratt plant, where the company’s liverwurst is made, has been shuttered since late July amid the investigation into how the outbreak occurred.
In the September 13 update, Boar’s Head explained that:
[O]ur investigation has identified the root cause of the contamination as a specific production process that only existed at the Jarratt facility and was used only for liverwurst. With this discovery, we have decided to permanently discontinue liverwurst.
While the statement seems to offer some closure on the outbreak’s source, previously released inspection reports described a facility riddled with sanitation failures. Between August 1, 2023, and August 2, 2024, the facility was cited for 69 violations, which included water leaks, mold in numerous places, algal growth, “meat buildup” caking equipment, and walls that were also crawling with flies and gnats, sightings of other insects, rancid smells, trash and debris on the floors, and even “ample amounts of blood in puddles.”
The New York Times also reported that a 2022 inspection found that the plant posed an “imminent threat” to public health and that inspectors cited “extensive rust, deli meats exposed to wet ceilings, green mold and holes in the walls.”
Cross-contamination
The document newly released by Boar’s Head is a letter dated July 31 from the US Department of Agriculture’s Food Safety and Inspection Service notifying the company that the Jarratt facility was suspended. The basis of the suspension was an inspection finding from July 24 and 25 of L. monocytogenes contaminating a pallet jack in a large room where ready-to-eat meats were processed. The room was a common area not specific to liverwurst processing and was deemed by Boar’s Head to be “low risk” for Listeria.
Meats from eight processing lines were in the room, with lines 1 through 4 on the left side and 5 through 8 on the right, handling hot dogs and other small sausages. The contaminated pallet jack was designated for production line 2, which was handling Beechwood Hams, and was used to move racks of hams from blast coolers to production lines in the processing room.
However, inspectors noted that the pallet jacks and product racks in the room weren’t kept to designated production lines, and instead, employees moved them between all of the lines and all of the blast coolers, enabling cross-contamination. And, while the equipment was moved around, people did, too. Although employees typically stuck to one production line, they would sometimes move between lines, and there were no procedures for employees to change personal protective equipment (PPE)—gloves, disposable aprons, and arm covers—when they switched. Inspectors saw them switching without changing their PPE.
“They also observed employees who freely move between all lines without directly interacting with product such as those removing garbage, removing product debris from the floors, removing condensation from overhead structures, or performing maintenance,” the USDA officials wrote.
Outbreak spread
Given that this was in a room full of meats that were supposedly ready to eat, the USDA concluded that Boar’s Head “failed to maintain sanitary conditions” and that its Listeria control program was “ineffective.”
To date, 57 people from 18 states have been sickened. All 57 were hospitalized, and nine people died. The Centers for Disease Control and Prevention reported that health officials have interviewed 44 people sickened during the outbreak, who said they ate various deli-sliced meats. Only 25 reported eating deli-sliced liverwurst.
In light of the outbreak, Boar’s Head said it is revamping its safety and quality assurances at its other facilities and hiring experienced food safety experts. “You have our promise that we will work tirelessly to regain your trust and ensure that all Boar’s Head products consistently meet the high standards that you deserve and expect. We are determined to learn from this experience and emerge stronger.”
Enlarge/ A recall notice is posted next to Boar’s Head meats that are displayed at a Safeway store on July 31, 2024, in San Rafael, California.
Federal inspections found 69 violations—many grisly—at the Boar’s Head meat facility at the center of a deadly, nationwide Listeria outbreak that has now killed nine people, sickened and hospitalized a total of 57 across 18 states, and spurred the nationwide recall of more than 7 million pounds of meat.
The Jarratt, Virginia-based facility had repeated problems with mold, water leaks, dirty equipment and rooms, meat debris stuck on walls and equipment, various bugs, and, at one point, puddles of blood on the floor, according to inspection reports from the US Department of Agriculture’s Food Safety and Inspection Services. The reports were obtained by CBS News through a Freedom of Information Act Request. In all, the reports outline 69 violations just between the dates of August 1, 2023, and August 2, 2024.
The findings in the reports reveal the perfect conditions for the company’s meat to become contaminated with the germ behind the deadly outbreak, Listeria monocytogenes. This is a hardy germ that is ubiquitous in the environment, including in soil and water, and it spreads among people via the fecal-oral route. In healthy people, it usually only causes gastrointestinal infections. But for older people, newborns, and the immunocompromised, it can cause a life-threatening invasive infection with a fatality rate of around 17 percent. It’s also a significant danger to pregnant people, causing miscarriage, stillbirth, premature delivery, and life-threatening infections in newborns.
While it’s always lurking, L. monocytogenes especially plagues the food industry because it has the notable ability to reproduce at refrigerator temperatures—a condition that typically limits the growth of other nasty germs.
Buildup and bugs
In the Boar’s Head facility, L. monocytogenes appeared to have various opportunities to beef up its numbers. For one, the facility had a long track record of trash and meat debris in various places, which was sometimes reported alongside insect sightings. For instance, on June 10, an inspector entered the “pickle vat pump room” and noted “heavy meat buildup” on the walls, which were also crawling with flies and gnats. On the same day, an inspection of a different area found a rollup door with meat buildup on it, and a water pipe over the door leaked a steady stream of water down the wall and onto the floor. There was also a “steady line of ants” and an inventory of ladybugs, a cockroach, and a beetle of some sort. Earlier, on March 13, an inspection of a room next to where netted hams were handled, an inspector found trash and meat protein on the floor, including “whole pork muscles.”
Going back to August 8, 2023, an inspection likewise found processing lines covered in meat particles and trash. “Heavy discolored meat buildup” was found covering a hydraulic pump, and pieces of meat and fat clung to the support braces of a catwalk. An inspection-line scale had meat pieces and trash in it—and it smelled bad. “Multiple instances of meat were found around the department on the floor. As well as standing water containing a brown mud/dirt-like substance,” the inspection read.
The facility had numerous problems with water leaks and condensation, which fits with the other numerous sightings of mold. The facility temporarily fixed water pipe leaks by wrapping the pipes in plastic. On October 26, an inspector noticed a plastic-wrapped pipe in the cure cooler. The plastic was dated August 17, and there was “orange/brown water pooled in the lowest hanging point.”
Bubbles and blood
On January 9, the inspection of a holding cooler found spots of black mold as large as a quarter throughout the room. On July 23, an inspector noticed bubbled paint on the wall around employee hand-washing sinks. The bubbles were filled with water. And under the sinks, the inspector found black mold and pink mildew.
On July 17, the inspector found “green algal growth” in a puddle of standing water in a raw holding cooler. And on July 27, an inspector noted clear liquid leaking out from a square patch on the ceiling. Behind the patch, there were two other patches that were also leaking. An employee came and wiped the liquid away with a sponge, but it returned within 10 seconds. The employee wiped it again, and the liquid again returned within 10 seconds. Meanwhile, a ceiling fan mounted close by was blowing the leaking liquid onto uncovered hams in a hallway outside the room.
To top if off, a report on February 21 found a raw cooler with “ample amounts of blood in puddles on the floor” and a “rancid smell.”
According to USDA documents, the agency has not taken enforcement actions against Boar’s Head, and there is no data available on swab testing for Listeria at the Virginia facility. The plant has been shut down since late July after health investigators found the outbreak strain of L. monocytogenes in unopened containers of Boar’s Head liverwurst.
In a statement updated on August 29, Boar’s Head said, “We are conducting an extensive investigation, working closely with the USDA and government regulatory agencies, as well as with the industry’s leading food safety experts, to determine how our liverwurst produced at our Jarratt, Virginia facility was adulterated and to prevent it from happening again… We will not resume operations at this facility until we are confident that it meets USDA regulatory standards and Boar’s Head’s highest quality and safety standards.”
Enlarge/ Shelves sit empty where Boar’s Head meats are usually displayed at a Safeway store on July 31, 2024, in San Anselmo, California.
Over 7 million pounds of Boar’s Head brand deli meats are being recalled amid a bacterial outbreak that has killed two people. The outbreak, which began in late May, has sickened a total of 34 people across 13 states, leading to 33 hospitalizations, according to the US Department of Agriculture.
On June 26, Boar’s Head recalled 207,528 pounds of products, including liverwurst, beef bologna, ham, salami, and “heat and eat” bacon. On Tuesday, the Jarratt, Virginia-based company expanded the recall to include about 7 million additional pounds of meat, including 71 different products sold on the Boar’s Head and Old Country brand labels. The products were sold nationwide.
The meats may be contaminated with Listeria monocytogenes, a foodborne pathogen that is particularly dangerous to pregnant people, people over the age of 65, and people with compromised immune systems. Infections during pregnancy can cause miscarriage, stillbirth, premature delivery, or a life-threatening infection in newborns. For others who develop invasive illness, the fatality rate is nearly 16 percent. Symptoms of listeriosis can include fever, muscle aches, headache, stiff neck, confusion, loss of balance, and convulsions that are sometimes preceded by diarrhea or other gastrointestinal symptoms.
The problem was discovered when the Maryland Department of Health—working with the Baltimore City Health Department—collected an unopened liverwurst product from a retail store and found that it was positive for L. monocytogenes. In later testing, the strain in the liverwurst was linked to those isolated from people sickened in the outbreak.
According to the Centers for Disease Control and Prevention, six of the 34 known cases were identified in Maryland, and 12 were identified in New York. The other 11 states have only reported one or two cases each. However, the CDC expects the true number of infections to be much higher, given that many people recover without medical care and, even if people did seek care, health care providers do not routinely test for L. monocytogenes in people with mild gastrointestinal illnesses.
In the outbreak so far, there has been one case in a pregnant person, who recovered and remained pregnant. The two deaths occurred in New Jersey and Illinois.
In a statement on the company’s website, Boar’s Head said that it learned from the USDA on Monday night that L. monocytogenes strain in the liverwurst linked to the multistate outbreak. “Out of an abundance of caution, we decided to immediately and voluntarily expand our recall to include all items produced at the Jarratt facility. We have also decided to pause ready-to-eat operations at this facility until further notice. As a company that prioritizes safety and quality, we believe it is the right thing to do.”
The USDA said it is “concerned that some product may be in consumers’ refrigerators and in retail deli cases.” The USDA, the company, and CDC warn people not to eat the recalled products. Instead, they should either be thrown away or returned to the store where they were purchased for a full refund. And if you’ve purchased one of the recalled products, the USDA also advises you to thoroughly clean your fridge to prevent cross-contamination.
The highly pathogenic avian influenza H5N1 virus that spilled from wild birds into US dairy cows late last year may have recently seeped from a dairy farm in Colorado to a nearby poultry farm, where it then infected five workers tasked with culling the infected chickens
In a press briefing Tuesday, federal officials reported that four of the avian influenza cases have been confirmed by the Centers for Disease Control and Prevention, while the fifth remains a presumptive positive awaiting CDC confirmation.
All five people have shown mild illnesses, though they experienced variable symptoms. Some of the cases involved conjunctivitis, as was seen in other human cases linked to the H5N1 outbreak in dairy cows. Others in the cluster of five had respiratory and typical flu-like symptoms, including fever, chills, sore throat, runny nose, and cough. None of the five cases required hospitalization.
The virus infecting the five people is closely related to the virus infecting the chickens on the poultry farm, which, in turn, is closely related to virus seen in infected dairy herds and in other human cases that have been linked to the dairy outbreak. The affected poultry farm is in Colorado’s northern county of Weld, which has also reported about two dozen outbreaks of avian influenza in dairy herds.
Dairy to poultry hypothesis
In one fell swoop, Colorado’s poultry farm outbreak has more than doubled the number of human avian influenza cases linked to the dairy cow spillover, bringing the previous tally of four cases to nine. While officials have previously noted instances where it appeared that H5N1 on dairy farms had moved to nearby poultry farms, this appears to be the first time such spread has led to documented human infections.
The link between the poultry farm cases and neighboring dairy farms is still just a hypothesis, however, Nirav Shah, the principal deputy director at the CDC, emphasized to reporters Tuesday. “It is a hypothesis that needs and requires a full investigation. But that is a hypothesis at this point,” he said of the link between the dairy farms and the poultry farm. So far, there is no direct evidence of a specific source of the poultry farm’s infection, and the route of infection is also unclear.
Throughout the outbreak of H5N1 on dairy farms, officials have noted that the primary way the virus appears to spread to new farms is via the movement of cows, people, and machinery between those facilities. There remains no evidence of human-to-human transmission. But milk from infected cows has been found to be brimming with high levels of infectious virus, and milk-contaminated equipment is a prime suspect in the spread.
In the press briefing Tuesday, Eric Deeble, acting senior advisor for H5N1 response with the US Department of Agriculture, noted the poultry are very susceptible to avian influenza and are easily infected. “It does not take much to introduce this into a flock,” Deeble said. The USDA is now working on a “trace-back” investigation on how the Colorado poultry farm was infected.
Searing spread
As for how the farm workers specifically became infected with the virus, health officials pointed to high temperatures that prevented workers from donning protective gear. The poultry farm is a commercial egg layer operation with around 1.8 million birds. Given the presence of bird flu on the premises, all 1.8 million birds need to be culled, aka “depopulated.” This is being carried out using mobile carts with carbon dioxide gas chambers, a common culling method. Workers are tasked with placing the birds in the chambers, which only hold a few dozen birds at a time. In all, the method requires workers to have a high degree of contact with the infected birds, going from bird to bird and batch to batch with the carts.
Amid this grim task, temperatures in the area reached over 100° Fahrenheit, and massive industrial fans were turned on in the facility to try to cool things down. Between the heat and the fans, the approximately 160 people involved in the culling struggled to use personal protective equipment (PPE). The required PPE for the depopulation involves a full Tyvek suit, boots, gloves, goggles, and an N95 respirator.
“The difficulty with wearing all that gear in that kind of heat, you can imagine,” said Julie Gauthier, executive director for field operations at the USDA’s Animal and Plant Health Inspection Service (APHIS). The industrial fans blowing large amounts of air made it yet more difficult for workers to keep goggles and respirators on their faces, she said.
The CDC and the USDA are both involved in further investigations of the poultry farm outbreak. CDC’s Shah noted that the team the agency deployed to Colorado included an industrial hygienist, who can work on strategies to prevent further transmission.
To date, at least 161 herds in 13 states have tested positive for avian influenza since the dairy outbreak was confirmed in March. Since January 2022, when US birds first tested positive for the H5N1 virus, 99 million birds in the US have been affected in 48 states, which involved 1,165 individual outbreaks.
The US government will pay Moderna $176 million to develop an mRNA vaccine against a pandemic influenza—an award given as the highly pathogenic bird flu virus H5N1 continues to spread widely among US dairy cattle.
The funding flows through BARDA, the Biomedical Advanced Research and Development Authority, as part of a new Rapid Response Partnership Vehicle (RRPV) Consortium. The program is intended to set up partnerships with industry to help the country better prepare for pandemic threats and develop medical countermeasures, the Department of Health and Human Services said in a press announcement Tuesday.
In an announcement of its own Tuesday, Moderna noted that it began a Phase 1/2 trial of a pandemic influenza virus vaccine last year, which included versions targeting H5 and H7 varieties of bird flu viruses. The company said it expects to release the results of that trial this year and that those results will direct the design of a Phase 3 trial, anticipated to begin in 2025.
The funding deal will support late-stage development of a “pre-pandemic vaccine against H5 influenza virus,” Moderna said. But, the deal also includes options for additional vaccine development in case other public health threats arise.
“mRNA vaccine technology offers advantages in efficacy, speed of development, and production scalability and reliability in addressing infectious disease outbreaks, as demonstrated during the COVID-19 pandemic,” Moderna CEO Stéphane Bancel said in the announcement. “We are pleased to continue our collaboration with BARDA to expedite our development efforts for mRNA-based pandemic influenza vaccines and support the global public health community in preparedness against potential outbreaks.”
US health officials have said previously that they were in talks with Moderna and Pfizer about the development of a pandemic bird flu vaccine. The future vaccine will be in addition to standard protein-based bird flu vaccines that are already developed. In recent weeks, the health department has said it is working to manufacture 4.8 million vials of H5 influenza vaccine in the coming months. The plans come three months into the H5N1 dairy outbreak, which is very far from the initial hopes of containment.
Botched response
The US is badly fumbling its response to the unprecedented outbreak, drawing criticism from US-based and international experts alike. Genetic analyses suggest that the virus has been spreading among the country’s dairy cattle since late last year. But, it wasn’t until months later, on March 25, that the US Department of Agriculture confirmed the first four infected herds in two states (Texas and Kansas). Since then, the outbreak has spread to around 140 herds in 12 states—at least.
Some farms are refusing to test, and experts expect that there is a significant number of undocumented herd infections, particularly given the widespread detection of inactivated H5N1 in the commercial milk supply. Further, of the 140 herds with documented infections, federal officials do not know how many are still actively infected rather than recovered. It is unclear if infected cows can become reinfected, and if so, how quickly after an infection.
While the risk to the general public is considered to be low currently, farm workers are at higher risk of contracting the infection. To date, there have been three confirmed infections among dairy farm workers—one in Texas and two in Michigan, which has had a uniquely robust response to the outbreak. Still, with hundreds to thousands of farm workers at risk of contracting the virus, only 53 people in the country to date have been tested for H5 influenza.
In a presentation in London last month, global health leader Seth Berkley said it was “shocking to watch the ineptitude” of the US response to the H5N1 outbreak. He, like other experts, questioned whether the US public health community has learned or improved from the failures of the COVID-19 pandemic.
Similar to problems during the pandemic, a key barrier to the H5N1 response is resistance from farmers and farm workers to partner with state and federal health officials. Federal agencies have limited authority within states, but they have announced an array of assistance programs for dairy farms, including compensatory funding and access to personal protective equipment for farm workers. They have also issued guidance and restrictions to tighten biosecurity measures. But there has been little voluntary participation on both fronts.
For instance, officials figured out early in the outbreak that movement of cattle, workers, and equipment between farms is the main way H5N1 is spreading among dairies. In April, the USDA required testing of a portion of cows prior to their movement across state lines. But movement within states is governed by states. In a survey last month, which captured data from 54 percent of affected farms at the time, more than 60 percent of farmers said they continued to move cattle off their infected farms after the onset of clinical signs of infection in their animals.
The more the virus expands its footprint across US dairy farms, adapts to its newfound mammalian host, and comes in contact with humans, the more and more chances it has to leap to humans and gain the ability to spread among us.
In HHS’s Tuesday announcement of the Moderna award, Dawn O’Connell, assistant secretary for Preparedness and Response, spoke to the growing concern that the H5N1 outbreak could spark another pandemic. “The award made today is part of our longstanding commitment to strengthen our preparedness for pandemic influenza,” O’Connell said. “Adding this technology to our pandemic flu toolkit enhances our ability to be nimble and quick against the circulating strains and their potential variants.”
Four backyard alpacas in southern Idaho have tested positive for highly pathogenic avian influenza (HPAI) H5N1, marking the first time bird flu has been detected in members of the fleecy camelid family, according to the US Department of Agriculture.
On Tuesday, the USDA announced that the agency’s National Veterinary Services Laboratories confirmed the infection on a farm in Jerome County on May 16. While the infections are a first for the spitting llama relatives, the USDA said they weren’t particularly surprising. The alpacas were in close contact with HPAI-infected poultry on the farm, which were “depopulated” this month. Of 18 alpacas on the affected farm, only four were found to be infected. There were no deaths documented, according to a report the USDA submitted to the World Organization for Animal Health.
Genomic sequencing indicates that the H5N1 virus infecting the alpacas (B3.13) matches both the virus currently circulating among US dairy cows and the virus that infected birds on the farm.
The finding does not increase the threat of H5N1 to the general public, but it again highlights the virus’s alarming ability to readily spread to mammals. The USDA has documented hundreds of cases of H5N1 in a wide range of mammals since May 2022, when the outbreak strain began spreading in North America. In March, the USDA announced the unprecedented outbreak among dairy cows. But the agency has found the virus spreading in mink, raccoons, foxes, cats, seals, bears, mountain lions, bottlenose dolphins, goats, and coyotes, among other animals. With each new species and infection, H5N1 gains new opportunities to adapt to better infect and spread among mammals. And as the virus jumps to mammals in close contact with humans, the risk increases that the virus will have the opportunity to adapt to spread among humans.
The USDA and state officials continue to identify H5N1 in dairy herds. According to the latest data on the USDA’s tracking site, at least 66 dairy herds in nine states have been infected.
Researchers at the University of Wisconsin-Madison squirted raw H5N1-containing milk from infected cows into the throats of anesthetized laboratory mice, finding that the virus caused systemic infections after the mice were observed swallowing the dose. The illnesses began quickly, with symptoms of lethargy and ruffled fur starting on day 1. On day 4, the animals were euthanized to prevent extended suffering. Subsequent analysis found that the mice had high levels of H5N1 bird flu virus in their respiratory tracts, as well their hearts, kidneys, spleens, livers, mammary glands, and brains.
“Collectively, our data indicate that HPAI [Highly Pathogenic Avian Influenza] A(H5N1) virus in untreated milk can infect susceptible animals that consume it,” the researchers concluded. The researchers also found that raw milk containing H5N1 can remain infectious for weeks when stored at refrigerator temperatures.
Bird flu has not historically been considered a foodborne pathogen, but prior to the unexpected outbreak of H5N1 in US dairy cows discovered in March, it had never been found at high levels in a food product like milk before. While experts have stepped up warnings against drinking raw milk amid the outbreak, the mouse experiment offers some of the first data on the risks of H5N1 from drinking unpasteurized dairy.
Before the mouse data, numerous reports have noted carnivores falling ill with H5N1 after eating infected wild birds. And a study from March in the journal Emerging Infectious Diseases reported that over half of the 24 or so cats on an H5N1-infected dairy farm in Texas died after drinking raw milk from the sick cows. Before their deaths, the cats displayed distressing neurological symptoms, and studies found the virus had invaded their lungs, brains, hearts, and eyes.
While the data cannot definitely determine if humans who drink H5N1-contaminated raw milk will suffer the same fate as the mice and cats, it highlights the very real risk. Still, raw milk enthusiasts have disregarded the concerns. PBS NewsHour reported last week that since March 25, when the H5N1 outbreak in US dairy cows was announced, weekly sales of raw cow’s milk have ticked up 21 percent, to as much as 65 percent compared with the same periods a year ago, according to data shared by market research firm NielsenIQ. Moreover, the founder of California-based Raw Milk Institute, Mark McAfee, told the Los Angeles Times this month that his customers baselessly believe drinking H5N1 will give them immunity to the deadly pathogen.
In normal times, the Centers for Disease Control and Prevention and the Food and Drug Administration strongly discourage drinking raw milk. Without pasteurization, it can easily be contaminated with a wide variety of pathogens, including Campylobacter, Cryptosporidium, E. coli, Listeria, Brucella, and Salmonella.
Fortunately, for the bulk of Americans who heed germ theory, pasteurization appears completely effective at deactivating the virus in milk, according to thorough testing by the FDA. Pasteurized milk is considered safe during the outbreak. The US Department of Agriculture, meanwhile, reports finding no H5N1 in retail beef so far and, in laboratory experiments, beef patties purposefully inoculated with H5N1 had no viable virus in them after the patties were cooked to 145°F (medium) or 160°F (well done).
The US Department of Agriculture this week posted an unpublished version of its genetic analysis into the spillover and spread of bird flu into US dairy cattle, offering the most complete look yet at the data state and federal investigators have amassed in the unexpected and worrisome outbreak—and what it might mean.
The preprint analysis provides several significant insights into the outbreak—from when it may have actually started, just how much transmission we’re missing, stunning unknowns about the only human infection linked to the outbreak, and how much the virus continues to evolve in cows. The information is critical as flu experts fear the outbreak is heightening the ever-present risk that this wily flu virus will evolve to spread among humans and spark a pandemic.
But, the information hasn’t been easy to come by. Since March 25—when the USDA confirmed for the first time that a herd of US dairy cows had contracted the highly pathogenic avian influenza H5N1 virus—the agency has garnered international criticism for not sharing data quickly or completely. On April 21, the agency dumped over 200 genetic sequences into public databases amid pressure from outside experts. However, many of those sequences lack descriptive metadata, which normally contains basic and key bits of information, like when and where the viral sample was taken. Outside experts don’t have that crucial information, making independent analyses frustratingly limited. Thus, the new USDA analysis—which presumably includes that data—offers the best yet glimpse of the complete information on the outbreak.
Undetected spread
One of the big takeaways is that USDA researchers think the spillover of bird flu from wild birds to cattle began late last year, likely in December. Thus, the virus likely circulated undetected in dairy cows for around four months before the USDA’s March 25 confirmation of an infection in a Texas herd.
This timeline conclusion largely aligns with what outside experts previously gleaned from the limited publicly available data. So, it may not surprise those following the outbreak, but it is worrisome. Months of undetected spread raise significant concerns about the country’s ability to identify and swiftly respond to emerging infectious disease outbreaks—and whether public health responses have moved past the missteps seen in the early stages of the COVID-19 pandemic.
But another big finding from the preprint is how many gaps still exist in our current understanding of the outbreak. To date, the USDA has identified 36 herds in nine states that have been infected with H5N1. The good news from the genetic analysis is that the USDA can draw lines connecting most of them. USDA researchers reported that “direct movement of cattle based upon production practices” seems to explain how H5N1 hopped from the Texas panhandle region—where the initial spillover is thought to have occurred—to nine other states, some as far-flung as North Carolina, Michigan, and Idaho.
Enlarge/ Bayes factors for inferred movement between different discrete traits of H5N1 clade 2.3.4.4b viruses demonstrating the frequency of movement.
Enlarge/ Putative transmission pathways of HPAI H5N1 clade 2.3.4.4b genotype B3.13 supported by epidemiological links, animal movements, and genomic analysis.
Putative transmission pathways of HPAI H5N1 clade 2.3.4.4b genotype B3.13 supported by epidemiological links, animal movements, and genomic analysis. [/ars_img]The bad news is that those lines connecting the herds aren’t solid. There are gaps in which the genetic data suggests unidentified transmission occurred, maybe in unsampled cows, maybe in other animals entirely. The genetic data is clear that once this strain of bird flu—H5N1 clade 2.3.4.4 genotype B3.13 —hopped into cattle, it could readily spread to other mammals. The genetic data links viruses from cattle moving many times into other animals: There were five cattle-to-poultry jumps, one cattle-to-raccoon transmission, two events where the virus moved from cattle to domestic cats, and three times when the virus from cattle spilled back into wild birds.
“We cannot exclude the possibility that this genotype is circulating in unsampled locations and hosts as the existing analysis suggests that data are missing and undersurveillance may obscure transmission inferred using phylogenetic methods,” the USDA researchers wrote in their preprint.
