Clues From Bird Flu’s Ground Zero on Dairy Farms in the Texas Panhandle

Conor here: Present in the following piece from KFF Health News are all the classics from US pandemic response:

  1. The prioritization of commerce over public health.
  2. The inability to collect data.
  3. The distrust of the public health establishment for various reasons.
  4. Failure to err on the side of caution. In this case, the following piece notes that “Federal restrictions have triggered a backlash from farmers who find them unduly punishing, given that pasteurized milk and cooked beef from dairy cattle appear to pose no risk to consumers.”

But a study just released in The New England Journal of Medicine notes the following:

Heat treatment at 72°C was performed, with the default settings of the PCR thermocycler (i.e., preheated lid at 105°C) or with a metal lid (heated to 72°C) covering the PCR block (see the Supplementary Appendix for details). After heat treatment, samples were inoculated into embryonated chicken eggs or Madin–Darby canine kidney (MDCK) cells for virus detection. Under these conditions, heat treatment for 15 or 20 seconds reduced virus titers by more than 4.5 log units but did not completely inactivate the virus…

By Amy Maxmen, a public health local editor and correspondent at KFF Health News. She covers efforts to prevent disease and improve well-being outside of the medical system, and the obstacles that stand in the way. Originally published at KFF Health News.

In early February, dairy farmers in the Texas Panhandle began to notice sick cattle. The buzz soon reached Darren Turley, executive director of the Texas Association of Dairymen: “They said there is something moving from herd to herd.”

Nearly 60 days passed before veterinarians identified the culprit: a highly pathogenic strain of the bird flu virus, H5N1. Had it been detected sooner, the outbreak might have been swiftly contained. Now it has spread to at least eight other states, and it will be hard to eliminate.

At the moment, the bird flu hasn’t adapted to spread from person to person through the air like the seasonal flu. That’s what it would take to give liftoff to another pandemic. This lucky fact could change, however, as the virus mutates within each cow it infects. Those mutations are random, but more cows provide more chances of stumbling on ones that pose a grave risk to humans.

Why did it take so long to recognize the virus on high-tech farms in the world’s richest country? Because even though H5N1 has circulated for nearly three decades, its arrival in dairy cattle was most unexpected. “People tend to think that an outbreak starts at Monday at 9 a.m. with a sign saying, ‘Outbreak has started,’” said Jeremy Farrar, chief scientist at the World Health Organization. “It’s rarely like that.”

By investigating the origins of outbreaks, researchers garner clues about how they start and spread. That information can curb the toll of an epidemic and, ideally, stop the next one. On-the-ground observations and genomic analyses point to Texas as ground zero for this outbreak in cattle. To backtrack events in Texas, KFF Health News spoke with more than a dozen people, including veterinarians, farmers, and state officials.

An early indication that something had gone awry on farms in northwestern Texas came from devices hitched to collars on dairy cows. Turley describes them as “an advanced fitness tracker.” They collect a stream of data, such as a cow’s temperature, its milk quality, and the progress of its digestion — or, rather, rumination — within its four-chambered stomach.

What farmers saw when they downloaded the data in February stopped them in their tracks. One moment a cow seemed perfectly fine, and then four hours later, rumination had halted. “Shortly after the stomach stops, you’d see a huge falloff in milk,” Turley said. “That is not normal.”

Tests for contagious diseases known to whip through herds came up negative. Some farmers wondered if the illness was related to ash from wildfires devastating land to the east.

In hindsight, Turley wished he had made more of the migrating geese that congregate in the panhandle each winter and spring. Geese and other waterfowl have carried H5N1 around the globe. They withstand enormous loads of the virus without getting sick, passing it on to local species, like blackbirds, cowbirds, and grackles, that mix with migrating flocks.

But with so many other issues facing dairy farmers, geese didn’t register. “One thing you learn in agriculture is that Mother Nature is unpredictable and can be devastating,” Turley said. “Just when you think you have figured it out, Mother Nature tells you you do not.”

Cat Clues

One dairy tried to wall itself off, careful not to share equipment with or employ the same workers as other farms, Turley recalled. Its cattle still became ill. Turley noted that the farm was downwind of another with an outbreak, “so you almost think it has to have an airborne factor.”

On March 7, Turley called the Texas Animal Health Commission. They convened a One Health group with experts in animal health, human health, and agriculture to ponder what they called the “mystery syndrome.” State veterinarians probed cow tissue for parasites, examined the animals’ blood, and tested for viruses and bacteria. But nothing explained the sickness.

They didn’t probe for H5N1. While it has jumped into mammals dozens of times, it rarely has spread between species. Most cases have been in carnivores, which likely ate infected birds. Cows are mainly vegetarian.

“If someone told me about a milk drop in cows, I wouldn’t think to test for H5N1 because, no, cattle don’t get that,” said Thomas Peacock, a virologist at the Pirbright Institute of England who studies avian influenza.

Postmortem tests of grackles, blackbirds, and other birds found dead on dairy farms detected H5N1, but that didn’t turn the tide. “We didn’t think much of it since we have seen H5N1-positive birds everywhere in the country,” said Amy Swinford, director of the Texas A&M Veterinary Medical Diagnostic Laboratory.

In the meantime, rumors swirled about a rash of illness among workers at dairy farms in the panhandle. It was flu season, however, and hospitals weren’t reporting anything out of the ordinary.

Bethany Boggess Alcauter, director of research at the National Center for Farmworker Health, has worked in the panhandle and suspected farmworkers were unlikely to see a doctor even if they needed one. Clinics are far from where they live, she said, and many don’t speak English or Spanish — for instance, they may speak Indigenous languages such as Mixtec, which is common in parts of Mexico. The cost of medical care is another deterrent, along with losing pay by missing work — or losing their jobs — if they don’t show up. “Even when medical care is there,” she said, “it’s a challenge.”

What finally tipped off veterinarians? A few farm cats died suddenly and tested positive for H5N1. Swinford’s group — collaborating with veterinary labs at Iowa State and Cornell universities — searched for the virus in samples drawn from sick cows.

“On a Friday night at 9 p.m., March 22, I got a call from Iowa State,” Swinford said. Researchers had discovered antibodies against H5N1 in a slice of a mammary gland. By Monday, her team and Cornell researchers identified genetic fragments of the virus. They alerted authorities. With that, the U.S. Department of Agriculture announced that H5N1 had hit dairy cattle.

Genomic sequences from H5N1 viruses suggest the current bird flu epidemic started with a spillover from birds into cows in Texas, and then spread to other states within cattle. Routes and timing remain uncertain because of limited data. (KFF HEALTH NEWS MAY 15 SCREENSHOT OF NEXTSTRAIN.ORG)

Recalling rumors of sick farmworkers, Texas health officials asked farmers, veterinarians, and local health departments to encourage testing. About 20 people with coughs, aches, irritated eyes, or other flu-like symptoms stepped forward to be swabbed. Those samples were shipped to the Centers for Disease Control and Prevention. All but one were negative for H5N1. On April 1, the CDC announced this year’s first case: a farmworker with an inflamed eye that cleared up within days.

Thirteen dairy farms in the panhandle had been affected, said Brian Bohl, director of field operations at the Texas Animal Health Commission. Farmers report that outbreaks among the herds last 30 to 45 days and most cows return to milking at their usual pace.

The observation hints that herds gain immunity, if temporarily. Indeed, early evidence shows that H5N1 triggers a protective antibody response in cattle, said Marie Culhane, a professor of veterinary population medicine at the University of Minnesota. Nonetheless, she and others remain uneasy because no one knows how the virus spreads, or what risk it poses to people working with cattle.

Although most cows recover, farmers said the outbreaks have disrupted their careful timing around when cattle milk, breed, and birth calves.

Farmers want answers that would come with further research, but the spirit of collaboration that existed in the first months of the Texas outbreak has fractured. Federal restrictions have triggered a backlash from farmers who find them unduly punishing, given that pasteurized milk and cooked beef from dairy cattle appear to pose no risk to consumers.

The rules, such as prohibiting infected cattle from interstate travel for 30 days, pose a problem for farmers who move pregnant cattle to farms that specialize in calving, to graze in states with gentler winters, and to return home for milking. “When the federal order came out, some producers said, ‘I’m going to quit testing,’” Bohl said.

In May, the USDA offered aid, such as up to $10,000 to test and treat infected cattle. “The financial incentives will help,” Turley said. But how much remains to be seen.

Federal authorities have pressed states to extract more intel from farms and farmworkers. Several veterinarians warn such pressure could fracture their relationships with farmers, stifling lines of communication.

Having fought epidemics around the world, Farrar cited examples of when strong-arm surveillance pushed outbreaks underground. During an early 2000s bird flu outbreak in Vietnam, farmers circumvented regulations by moving poultry at night, bribing inspection workers, and selling their goods through back channels. “Learning what drivers and fears exist among people is crucial,” Farrar said. “But we always seem to realize that at a later date.”

A powerful driver in the U.S.: Milk is a $60 billion industry. Public health is also bound to bump up against politics in Texas, a state so aggrieved by pandemic restrictions that lawmakers passed a bill last year barring health officials from recommending covid-19 vaccines.

Texas Agriculture Commissioner Sid Miller said that when he heard that federal agents with the CDC and USDA were considering visits to farms — including those where farmers reported the cattle had recovered — he advised against it. “Send federal agents to dairy that’s not sick?” he said. “That doesn’t pass the smell test.”

From Texas to the Nation

Peacock said genomic analyses of H5N1 viruses point to Texas as ground zero for the cattle epidemic, emerging late last year.

“All of these little jigsaw puzzle pieces corroborate undetected circulation in Texas for some time,” said Peacock, an author on one report about the outbreak.

Evidence suggests that either a single cow was infected by viruses shed from birds — perhaps those geese, grackles, or blackbirds, he said. Or the virus spilled over from birds into cattle several times, with only a fraction of those moving from cow to cow.

Sometime in March, viruses appear to have hitched a ride to other states as cows were moved between farms. The limited genomic data available links the outbreak in Texas directly to others in New Mexico, Kansas, Ohio, North Carolina, and South Dakota. However, the routes are imprecise because the USDA hasn’t attached dates and locations to data it releases.

Researchers don’t want to be caught off guard again by the shape-shifting H5N1 virus, and that will require keeping tabs on humans. Most, if not all, of about 900 people diagnosed with H5N1 infections worldwide since 2003 acquired it from animals, rather than from humans, Farrar said. About half of those people died.

Occasional tests of sick farmworkers aren’t sufficient, he said. Ideally, a system is set up to encourage farmworkers, their communities, and health care workers to be tested whenever the virus hits farms nearby.

“Health care worker infections are always a sign of human-to-human transmission,” Farrar said. “That’s the approach you want to take — I am not saying it’s easy.”

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    1. ajc

      Because there is paperwork and receipts showing where poultry litter originates, and if any of those chicken farms had H5N1 not detected by the farm itself with the attendant mass cull would have been news. There is a robust H5N1 surveillance regime with chicken farms that the farmers support because an uncontrolled outbreak could take out a lot of farms and farmers.

      Cow ponds are numerous across Texas range plus stock tanks are routinely visited by and pooped in by all manner of birds/wildlife. They are filled with rain or well water which doesn’t have the chlorine or amines used to sanitize water for public consumption.

  1. jefemt

    Mad cow, angry chicken. So much pent-up frustration these days! A different, metaphorical spillover

  2. Arkady Bogdanov

    This is very interesting. I had been consistently seeing reports that the virus invaded the udders and “stayed there” and produced no noticeable symptoms in cattle. This is obviously bullshit if the rumen is shutting down (rumen is very temperature sensitive- to the point where I have heard farmers discuss the optimum drinking water temperature for cows). So to me this suggests that the animals core temperature is being affected (fever). As to the farm trying to isolate itself from other farms. I will bet they never gave a thought to their barn cats (I have NEVER seen a dairy operation that did not include a number of cats for rodent control, and all of the cats come and go as they please). I would certainly not rule out airborne transmission, but I find it hard to believe that the virus could drift in the open air and sunlight from one farm to another. I strongly suspect the cats are moving it (perhaps with some help from rodents and insect parasites- like fleas and ticks). Note that the general public also often dumps unwanted cats at farms- this is so common that every farm experiences it.
    I was blown away while at a small beef farm the other day (about 50 breeding cows)- while inspecting some infrastructure that was just completed, the farmer and I were speaking about his herd genetics (very common conversation that can go on for a long time- farmers love talking genetics) and he pointed to 4 or 5 different animals that he told me he had recently purchased- EACH FROM A DIFFERENT AREA IN THE MIDWEST. Now this particular farmer is not someone I would claim to be a serious planner or intellectual, but I was stunned to hear that nonetheless, and given his political predilections I did not remark on it, but I was screaming out WTF IS WRONG WITH YOU? in my head- as most farmers I know are worried about the situation. It only takes one guy in a give region like this guy to mess things up, but there you are. Every area has them.

  3. lambert strether

    > One dairy tried to wall itself off, careful not to share equipment with or employ the same workers as other farms, Turley recalled. Its cattle still became ill. Turley noted that the farm was downwind of another with an outbreak, “so you almost think it has to have an airborne factor.”

    5. droplet dogma

    1. Arkady Bogdanov

      Agree, however- there are vectors that I would suspect before airborne (I believe airborne transmission might very well dominate on individual farms, but I don’t seeing that being a vector for farm to farm transmission). Manure is spread daily on many farms, and on farms with better infrastructure, in multi-week long bursts in the spring and fall. Equipment drops manure hear and there as it is moved, and it is inevitably on the farm driveway- a great many deliveries occur on farms (mailman, feed store, spare parts, fertilizers, chemicals, UPS, Fedex, salespersons, gov agency people, contractors, equipment servicers, people just visiting- then people get out of vehicles and walk around. I keep expecting to be told that I have to start using biosecurity protocols for every farm visit I make (disposable shoe booties, or cleaning my shoes with chlorox and soap when I leave every farm- It’s PITA and likely once this order arrives, my organization will literally be the only ones in the country that does it). So there are a great many ways this could be transported from farm to farm- I still suspect the barn cats/rodents/fleas/ticks are the prime vector though. Every farm keeps a large group of cats in the barn, and they come and go and roam as they please. We may never know for sure. Many farmers are talking about this- and the better managers are taking the precautions they can. As someone who visits farms over a good-sized geographic area in Pennsylvania, I have been paying as close attention as I can (my kids once counted the contacts in my phone- I have over 400 farmers in there, so I do get around to alot of farms). The situation was even broached at a general meeting between a few farmers and some state legislators a couple of weeks ago, that I was present at. No responses were discussed, but concerns were aired. I will keep you all posted if I think I come across or hear anything that I think warrants attention.

      1. Raymond Sim

        We know from the Texas vet who discovered the outbreak that one of the principle symptoms is respiratory distress. Also virus was found in lung tissue of a necropsied cow. Since there is evidence for transmission without direct contact I think airborne transmission is more than merely plausible.

        I’m absolutely with you on the barn cats, but I think you may need to recalibrate your mental models regarding the potential for airborne transmission. The gap between what mathematical models (and some empirical evidence) indicate is possible, and what most of us were imbued with as “common sense” is very large.

        1. Arkady Bogdanov

          You misunderstand me- I absolutely believe airborne transmission is likely occurring, I just find it hard to believe that it is going to travel 1-2 miles (or more) through the open air between farms. Some living organism has to inhale it on the first farm, become infectious and carry it to another farm, and then exhale it on the second farm (or transfer it between organisms somewhere in the middle). Or, it is being moved from farm to farm via bodily fluids (manure on tires/feet/etc). Multiple transmission modes are likely occurring.

          1. Raymond Sim

            If 500 healthy cows spend 30 minutes of a calm night in the exhalation plume of 100 sick cows 2 miles distant, what are the odds at least 1 cow in the healthy herd gets an infectious dose?

            To my mind the big wild card is the behavior of the plume. Depending on atmospheric conditions they can be far more coherent than one might anticipate.

            1. Arkady Bogdanov

              Dairy cows might be allowed out during the day to graze, but they are not confined to a small area outside as you assume. The average herd size, nation wide, is around 60-80 cows, and they would be spread out over several acres if on pasture, so I do not see a “plume” forming. At night, they are usually inside the parlor and for several hours each milking as well. As dairy herd size goes up, they are less and less likely to be outside at all. Even 100 cow dairies typically keep the cows in a building at all times. On dairy CAFOs, it is highly unlikely for cows to ever be outside (I will also point out that this was occurring during the winter- I’d bet money that the dairy animals were all inside being fed hay and silage- nothing was growing on pasture due to the temperatures). On small farms heifers and dry cows may be allowed to roam pastures during the summer, but in that case I would think the disease would be far less communicable as the cows are far more spread out. A pasture system has paddocks the cows rotate through, but a decently managed grazing system is sized to for about 1 cow for 3 acres or so, and that is in my area where we get lots of rain, in Texas the animal density on pasture is going to be far less because of the dry conditions that produce far less vegetation (Perhaps Amfortas could give us some actual stocking densities). Cows tightly packed on pasture grass will destroy the valuable grass in a matter of minutes- so this is not done. Animal density on pasture is very low. (in the case of a beef feedlot, if you were downwind and could smell the feedlot, you might have a case, and even then I would think the virus itself would be more diffuse and would travel less in a live state than the smell). I would compare a dairy pasture to a bunch of kids continuously playing soccer and never leaving that soccer field infecting another continuous soccer game even a half mile away. That is the animal density we are talking, and I am sorry- I do not think it is impossible to spread in that manner, but so unlikely as to be much more simply explained by someone observing one game, and then going to observe the other game, thus physically carrying the virus with them. As with humans, I would suspect that the vast majority of all transmission is occurring inside buildings (where aerosol transmission is probably rampant), with the transmission between buildings occurring because some individual animal is moving between the buildings. Apologies if I am not getting this across properly, but I think if you understood how these animals were managed on dairies, you would understand my point. I promise you, I am not an aerosol denier. What enrages me is that at one point, this could have very easily been contained, but lack of curiosity, lack of seriousness, a belief that disease spread is inevitable and unstoppable, and that people are wimps if they try to slow or halt any kind of spread has just made people shrug. My guess is that this disease has been in cows for far, far longer than almost everyone is assuming.

              1. Piotr Berman

                If cats can be a vector, perhaps the same is true for rodents, I am not sure what would you advise about barn cats. Even with confined cows, barns are visited by cats, rats, sparrows etc.

              2. Raymond Sim

                I’m not unfamiliar with dairy farms. I worked on one as a teenager in PA, in the course of which I was on the premises of a number of other dairy farms of varying sizes. And I’ve lived in Davis, California for 40 years, and have some idea of how things are done in arid climates as well.

                Where aerosols are concerned it’s not a question of whether a plume forms, it’s a matter of how rapidly it dissipates/how fast the virus dies. In calm air particularly the ability of such plumes to deliver an infectious dose over distance can be startling. So startling that people tend to want to regard the well-documented events we know of as freak occurences, rather than simply examples of what’s possible.

  4. redleg

    I’m surprised that there are that many dairy operations that close together in Texas. Dairy farming is the most water intensive kind of farming that i know of (excluding fish farms), and Texas is not known for its abundance of water. There are dairy operations in Minnesota, the Land of 10,000 Lakes (lol) that are draining local aquifers FFS. Maybe this will force the farmers to reconsider their operations and transition into something more resilient, although i doubt anything will change the “use until expended and discard” mindset of most people these days (Lambert’s Law of Neoliberalism).

    1. Arkady Bogdanov

      In this day and age, milk processing companies and cooperatives control the location of dairies- they do this because they want efficient trucking routes. For the last 10-15 years, they have been refusing to sign on isolated dairies, because the truck has to go out of its way, unless your dairy is large enough to fill a tanker on it’s own. These efforts have created situations where dairies basically exist in geographical rings around milk processing facilities and bulk milk aggregators. So you have regions with zero dairies and then you have regions with dairies, and you have isolated, ultra large CAFO operations (Wal Mart began a trend of setting these up, and they have collapsed dairy farming in entire states). Even so, small dairy farms are going to be placed miles apart. I cover 6 counties in Pennsylvania, and the closest two dairies that I can think of are a good 2-3 miles apart- other then these two, dairies are a good 5 to 10 miles apart, at least. As dairy size increases, this forces them to be even farther apart, as they need more land to grow crops and forage. In drier areas, such as Texas, they are going to be spaced out even further. This is why I believe there is a more complicated transmission chain between dairies than most people assume. Someone or something has to be carrying it between them, quite possibly involving intermediate transmission.

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