California bird flu emergency declaration highlights a larger issue

In the ongoing outbreak of H5N1 bird flu among the nation’s dairy cattle, federal officials have consistently expressed confidence that they know enough about how the virus is spreading to put a stop to it. But among epidemiologists and other infectious disease experts, there has been skepticism that the U.S. Department of Agriculture’s theory of viral transmission is telling the whole story. And perhaps there is no greater cause for scrutiny than what’s currently happening in California.

Since the first identification of three infected herds there in late August, California authorities have found the virus in 659 of the state’s 984 dairies — about half of them in the last month alone. 

On Wednesday, in response to the explosive spread of the virus among the state’s dairy herds, California Gov. Gavin Newsom declared a state of emergency. “This proclamation is a targeted action to ensure government agencies have the resources and flexibility they need to respond quickly to this outbreak,” Newsom said in a statement.

California, which despite being the nation’s largest dairy-producing state had avoided the virus for the first five months of the outbreak, now makes up the vast majority of reported dairy cattle infections. 

“While some farmers may have been less strict” in following USDA precautions to prevent the spread of H5N1, “I personally know a fair number of producers that pulled out all the stops, followed every suggestion, came up with novel protections of their own,” Mike Payne, a food animal veterinarian and biosecurity expert with the University of California, Davis’ Western Institute for Food Safety and Security, told STAT in an email. “They still got infected and were enormously disheartened and frustrated.” 

Early on in the outbreak, genetic analyses suggested that the virus was expanding its footprint primarily through the movement of cattle across state lines. In April, the USDA moved to limit that through a federal order requiring testing of lactating cattle prior to interstate movement, although farmers didn’t have to test every member of larger herds and could choose which animals to test. As the virus continued to pop up in new places, the USDA conducted surveys of farmers in hotspots like Michigan and Colorado, where state authorities were more aggressively testing for the virus. 

In July, Eric Deeble, the acting senior adviser for the H5N1 response at the USDA, told reporters that the agency’s investigations had shown the movement of workers between farms and shared use of equipment and vehicles, in addition to the transport of cows, was spreading the virus. Cut off those routes — by increasing sanitation and limiting personnel — and the virus should be contained. “All the signs that we have are, with good biosecurity, with good farmer participation, we will be able to eliminate this,” Deeble said. 

In a press call two months later, Deeble attributed a decline in the rate of new infections in Colorado and Michigan primarily to a “greater understanding among producers and state animal health professionals about the need for biosecurity” as well as the federal order restricting the interstate movement of lactating dairy cattle.

On Thursday, a USDA spokesperson told STAT in an email that all the research to date suggests that transmission of H5N1 between cattle is largely believed to be due to fomites — that is, objects that come into contact with cattle that carry the virus on them, for example milking equipment and people’s clothing. “Transmission between farms is likely related to normal business operations such as people, vehicles and other farm equipment frequently moving between premises,” the spokesperson said. “That’s why strong biosecurity is critically important in stopping the spread of the virus and why USDA is strongly encouraging farmers to heed biosecurity recommendations.”

But some experts suspect that the end-of-summer slowdown had more to do with the virus running out of new, immune-naive herds to hop into. 

In Colorado, for instance, H5N1 went through 74% of the state’s herds before it began to peter out. Payne believes that even with all the measures California farmers are taking, the virus won’t slow down until it has infected 80% to 90% of the state’s herds.

Reports from Payne and others that cows are being infected despite diligent preventive measures indicate that there are multiple routes of transmission, some of which aren’t being accounted for in current mitigation measures, said Seema Lakdawala, an associate professor in the department of microbiology and immunology at Emory University School of Medicine. She bristles at the USDA’s theory that fomites carried on people’s clothing could play a significant role in spreading the disease. 

“It’s just not an efficient transmission route for the virus to go from a porous surface like your clothes up into the mammary gland of a cow,” she said. More likely, when it comes to personnel, is that workers are contracting the virus themselves and spreading it to other animals, she said. On the farms she’s visited, Lakdawala has observed workers wearing the same pair of gloves for an entire day of milking, and rarely seen people wear eye or face protection. “They’re using the same rags to dry the cows and wipe their own faces so there’s a lot of potential contaminants happening right there.”

But likely the bigger issue, she said, is new cattle being brought onto farms that don’t have symptoms of the virus but are already infected. While USDA has rules about testing herds prior to interstate travel, no such rules exist to move cows between farms in the same state. 

After the first H5N1 detection in California, state officials began testing bulk milk tanks of nearby operations, a strategy that identified many additional infections. But bulk tanks contain milk from many animals, so a few infections could go undetected on account of the dilution effect. “The tank a cow came from could be negative, but that cow could still be infected and you wouldn’t know because we’re not testing on a cow-by-cow level,” Lakdawala said.

Scientists are beginning to look into other hypotheses. According to Payne, research is underway to better understand if the virus is being transmitted between farms through local wildlife or infectious aerosol-laced dust plumes. But much about how the bird flu is spreading remains unknown. 

“Any ‘expert’ who really is following the outbreak and scientific trials here in California will tell you we think we know some of the ways the virus is being transferred from herd to herd, but not all of them,” Payne said. “Honestly, there’s probably more we don’t understand than we actually do know.”

Jennifer Nuzzo, an epidemiologist and director of Brown University’s Pandemic Center, echoed that in a webinar Tuesday hosted by the Boston University Center on Emerging Infectious Disease. “I have not seen a very compelling explanation for how this thing is moving between farms,” Nuzzo said in response to a question from STAT. “We just don’t know. And not knowing makes it hard to stay ahead of the virus and it also makes it hard to protect the workers.”

During a call with reporters Friday, California state veterinarian Annette Jones said that there are 40 research projects — many funded by the USDA — currently underway in the state to understand if there are additional modes of transmission between farms that animal health authorities are missing. “We know for sure this virus can travel in a livestock trailer, either in a cow or just infected material,” Jones said. “But sometimes it just seems like something else is causing the spread as well.”

She also noted that cows may be asymptomatic for a number of weeks—shedding virus into milk long before they show clinical signs like fever and a drop in milk production. This could have contributed to infected animals unwittingly being moved to new farms during the early stages of California’s outbreak. 

Although the agriculture department is now testing the bulk milk tanks of all 984 dairies in the state on a weekly basis, that strategy is new as of a few weeks ago. Prior to that, only dairies within a few miles of quarantined operations were subject to proactive monitoring. California’s dairy industry, which has undergone consolidation in recent years, also tends toward raising cows outdoors more so than some other dairy-producing states, Jones added. “There’s just movement and access and they’re connected, that’s really leading to the spread,” she said. 

On the human health side, state and local health departments have been distributing millions of pieces of protective gear to California’s dairy industry workforce. But advocates for farmworkers would like to see some of the resources newly mobilized by the emergency declaration going toward compensating dairy workers for getting tested for H5N1 and covering their wages if they test positive so they’ll stay home until the infection clears. “Right now it’s a bad gamble for workers,” said Elizabeth Strater, a spokesperson for United Farm Workers, which is why many of them are actively avoiding testing or reporting symptoms to employers and public health authorities. 

Figuring out a model that encourages farmworkers to participate in the public health response is key to preventing H5N1 from becoming a more widespread problem. “They are the firewall between this novel virus and the general public,” Strater said.

As of Thursday, the USDA has confirmed 866 herds in 16 states since the outbreak was first detected in late March. But farmers in many parts of the country have resisted testing for the virus, leading to a widespread belief that more farms and more states have had outbreaks than have reported them. Several serology studies, where blood samples from farm workers were tested for antibodies, have confirmed that there have been missed infections. The outbreak — the first one where H5N1 is spreading in a mammalian species with which humans have frequent close exposures — raises concerns about creating unchecked opportunities for the avian virus to adapt to human hosts. 

So far this year, 61 human cases of H5N1 bird flu have been confirmed in the U.S. Most have been in people in California who worked on affected dairy farms or were hired to cull infected poultry flocks, and until recently, all have had very mild symptoms. But on Wednesday, the Centers for Disease Control and Prevention confirmed the country’s first known severe infection, in a person in Louisiana believed to have contracted the virus through contact with sick or dead birds in a backyard flock. The unidentified individual, who is over the age of 65 and has underlying health conditions, is in critical condition with severe respiratory illness.

The uptick in human cases is one of the reasons that the USDA has begun requiring farms to provide milk for testing when asked. On December 6, the agency announced it was instituting a new mandatory national milk testing program intended to provide a clearer picture of how entrenched the virus is in the country’s dairy industry. Speaking to reporters on Wednesday, Deeble said that the move came in response to the continued spread of H5N1 among California’s dairy cattle, as well as growing evidence that the virus can be detected in milk prior to cows showing signs of illness. 

“It’s a combination of these things that compelled us to increase the testing and to make it national in the way that it is now,” Deeble said. The program should provide “a really important opportunity to help farmers detect the disease before clinical signs are present in a herd,” he added. 

Lakdawala agreed that the new testing strategy will improve understanding of how far the virus has spread as well as what’s driving it. But nine months into the outbreak, she worries it may be arriving too late.

“The fact that we’ve had so many human infections is starting to concern, rightfully so, most public health agencies,” Lakdawala said. “There’s more pressure now to solve these questions then there probably was in April or May when we could have maybe actually contained the outbreak.”

This story has been updated with comments made Friday by the California state veterinarian.