Virus World

Testing conducted by the FDA on pasteurized commercially purchased milk has found genetic evidence of the H5N1 bird flu virus, the agency confirmed Tuesday. But the testing, done by polymerase chain reaction, or PCR, cannot distinguish between live virus or fragments of viruses that could have been killed by the pasteurization process. The agency said it has been trying to see if it could grow virus from milk found to contain evidence of H5N1, which is the gold standard test to see if there is viable virus in a product. The lengthy statement the agency released does not explicitly say FDA laboratories were unable to find live virus in the milk samples, but it does state that its belief that commercial, pasteurized milk is safe to consume has not been altered by these findings. “To date, we have seen nothing that would change our assessment that the commercial milk supply is safe,” the statement said.

The document was long on assurances but short on details of what has been undertaken or found. It does not specify how many commercial samples were taken or in how many markets, nor does it indicate what percentage of the samples were PCR-positive for H5N1. The statement did not indicate if the testing suggested the amounts of viral genetic material in the milk were low or high. Furthermore, the statement did not reveal if the milk products were purchased in parts of the country where outbreaks have occurred, or in areas where cows haven’t been seen to have been infected. The FDA did say it is testing milk from infected animals, in the processing system, and from store shelves with the goal of producing a “large representative national sample” of the milk supply. Beyond assessing the safety of the supply, such a sample could enable the agency to construct a more robust picture of H5N1’s spread among dairy cows nationally. The agency emphasized that testing of commercially available milk is ongoing, and this includes efforts to discern any potential differences between different dairy products, such as cream and whole milk....

U.S. regulators confirmed that sick cattle in Texas, Kansas and possibly in New Mexico contracted avian influenza. They stressed that the nation’s milk supply is safe. A highly fatal form of avian influenza, or bird flu, has been confirmed in U.S. cattle in Texas and Kansas, the Department of Agriculture announced on Monday. It is the first time that cows infected with the virus have been identified. The cows appear to have been infected by wild birds, and dead birds were reported on some farms, the agency said. The results were announced after multiple federal and state agencies began investigating reports of sick cows in Texas, Kansas and New Mexico. In several cases, the virus was detected in unpasteurized samples of milk collected from sick cows. Pasteurization should inactivate the flu virus, experts said, and officials stressed that the milk supply was safe.

“At this stage, there is no concern about the safety of the commercial milk supply or that this circumstance poses a risk to consumer health,” the agency said in a statement. Outside experts agreed. “It has only been found in milk that is grossly abnormal,” said Dr. Jim Lowe, a veterinarian and influenza researcher at the College of Veterinary Medicine at the University of Illinois at Urbana-Champaign. In those cases, the milk was described as thick and syrupy, he said, and was discarded. The agency said that dairies are required to divert or destroy milk from sick animals....

USDA report (March 25, 2024):

https://www.aphis.usda.gov/aphis/newsroom/news/sa_by_date/sa-2024/hpai-cattle 

The USDA tested 30 samples from states with herds infected by H5N1. Tests of ground beef purchased at retail stores have been negative for bird flu so far, the U.S. Department of Agriculture announced Wednesday, after studying meat samples collected from states with herds infected by this year's unprecedented outbreak of the virus in cattle. The results "reaffirm that the meat supply is safe," the department said in a statement published late Wednesday after the testing was completed. Health authorities have cited the "rigorous meat inspection process" overseen by the department's Food Safety Inspection Service, or FSIS, when questioned about whether this year's outbreak in dairy cattle might also threaten meat eaters.    "FSIS inspects each animal before slaughter, and all cattle carcasses must pass inspection after slaughter and be determined to be fit to enter the human food supply," the department said. The National Veterinary Services Laboratories tested 30 samples of ground beef in total, which were purchased at retail outlets in states with dairy cattle herds that had tested positive.

To date, dairy cattle in at least nine states — Colorado, Idaho, Kansas, Michigan, New Mexico, North Carolina, Ohio, South Dakota and Texas — have tested positive for H5N1, which is often lethal to poultry and other animals, like cats, but has largely spared cattle aside from sometimes disrupting their production of milk for a few weeks.  A USDA spokesperson said the ground beef they tested came from stores in only eight of those states. Colorado was only confirmed to have H5N1 in a dairy cow after USDA had collected the samples. The spokesperson did not comment on whether beef from stores in additional states would be sampled. More results from the department related to bird flu in beef are expected soon. Samples collected from the beef muscle of dairy cows condemned by inspectors at slaughter facilities are still being tested for the virus. The department is also testing how cooking beef patties to different temperatures will kill off the virus. "I want to emphasize, we are pretty sure that the meat supply is safe. We're doing this just to enhance our scientific knowledge, to make sure that we have additional data points to make that statement," Dr. Jose Emilio Esteban, USDA under secretary for food safety, told reporters Wednesday.

The studies come after the USDA ramped up testing requirements on dairy cattle moving across state lines last month in response to the outbreak.  Officials said that was in part because it had detected a mutated version of H5N1 in the lung tissue of an asymptomatic cow that had been sent to slaughter. While the cow was blocked from entering the food supply by FSIS, officials suggested the "isolated" incident raised questions about how the virus was spreading. Signs of bird flu have also made its way into the retail dairy supply, with as many as one in five samples of milk coming back positive in a nationwide Food and Drug Administration survey.  The FDA has chalked those up to harmless fragments of the virus left over after pasteurization, pointing to experiments showing that there was no live infectious virus in the samples of products like milk and sour cream that had initially tested positive. But the discovery has worried health authorities and experts that cows could be flying under the radar without symptoms, given farms are supposed to be throwing away milk from sick cows. One herd that tested positive in North Carolina remains asymptomatic and is still actively producing milk, a spokesperson for the state's Department of Agriculture and Consumer Services told CBS News.  It remains unclear how H5N1 has ended up in the milk supply. Don Prater, the FDA's top food safety official, said Wednesday that milk processors "can receive milk from hundreds of different farms, which may cross state lines," complicating efforts to trace back the virus. "This would take extensive testing to trace it that far," Bailee Woolstenhulme, a spokesperson for the Utah Department of Agriculture and Food, told CBS News.  Woolstenhulme said health authorities are only able to easily trace back milk to so-called "bulk tanks" that bottlers get. "These bulk tanks include milk from multiple dairies, so we would have to test cows from all of the dairies whose milk was in the bulk tank," Woolstenhulme said.

In early March, veterinarian Barb Petersen noticed the dairy cows she cared for on a Texas farm looked sick and produced less milk, and that it was off-color and thick. Birds and cats on the farm were dying, too. Petersen contacted Kay Russo at Novonesis, a company that helps farms keep their animals healthy and productive. “I said, you know, I may sound like a crazy, tinfoil hat–wearing person,” Russo, also a veterinarian, recalled at a 5 April public talk sponsored by her company. “But this sounds a bit like influenza to me.” She was right, as Petersen and Russo soon learned. On 19 March, birds on the Texas farm tested positive for H5N1, the highly pathogenic avian flu that has been devastating poultry and wild birds around the world for more than 2 years. Two days later, tests of cow milk and cats came back positive for the same virus, designated 2.3.4.4b. “I was at Target with my kids, and a series of expletives came out of my mouth,” Russo said. Now, 3 weeks into the first ever outbreak of a bird flu virus in dairy cattle, Russo and others are still dismayed—this time by the many questions that remain about the infections and the threat they may pose to livestock and people, and by the federal response. Eight U.S. states have reported infected cows, but government scientists have released few details about how the virus is spreading.

In the face of mounting criticism about sharing little genetic data—which could indicate how the virus is changing and its potential for further spread—the U.S. Department of Agriculture (USDA) did an unusual Sunday evening dump on 21 April of 202 sequences from cattle into a public database. (Some may be different samples from the same animal.) And despite public reassurances about the safety of the country’s milk supply, officials have yet to provide supporting data.  The cow infections, first confirmed by USDA on 25 March, were “a bit of an inconvenient truth,” Russo says. Taking and testing samples, sequencing viruses, and running experiments can take days, if not weeks, she acknowledges. But she thinks that although officials are trying to protect the public, they are also hesitant to cause undue harm to the dairy and beef industries. “There is a fine line of respecting the market, but also allowing for the work to be done from a scientific perspective,” Russo says.

Only one human case linked to cattle has been confirmed to date, and symptoms were limited to conjunctivitis, also known as pink eye. But Russo and many other vets have heard anecdotes about workers who have pink eye and other symptoms—including fever, cough, and lethargy—and do not want to be tested or seen by doctors. James Lowe, a researcher who specializes in pig influenza viruses, says policies for monitoring exposed people vary greatly between states. “I believe there are probably lots of human cases,” he says, noting that most likely are asymptomatic. Russo says she is heartened that the Centers for Disease Control and Prevention has “really started to mobilize and do the right thing,” including linking with state and local health departments, as well as vets, to monitor the health of workers on affected farms.

As farms in more states began to report infected dairy cows last month, one theory held migratory birds were carrying the virus across the country and introducing it repeatedly to different dairy herds. But Lowe dismisses the idea as “some fanciful thinking by some cow veterinarians and some cow producers” who hoped to “protect the industry.”

Richard Webby, an avian influenza researcher at St. Jude Children’s Research Hospital, notes that available data on the virus’ genetic sequence show “no smoking guns”—mutations that could enable it to jump readily from birds to cows. At a 4 April meeting organized by a group known as the Global Framework for the Progressive Control of Transboundary Animal Diseases, Suelee Robbe Austerman of USDA’s National Veterinary Services Laboratory said “a single spillover event or a couple of very closely related spillover events” from birds is more likely. The cow virus—which USDA has designated 3.13—could then have moved between farms as southern herds were moved northward for the spring, perhaps spreading from animal to animal on milking equipment. Lowe notes that researchers at Iowa State necropsied infected cows and found no virus in their respiratory tracts, which could enable spread through the air.

USDA considers H5N1 in poultry a “program disease,” which means it is foreign to the country and subject to regulations to control it. But the agency has made no such determination for the cow disease, which means the federal government has no power to restrict movement of cattle or to require testing and reporting of infected herds or of the humans who work with them. As a result, confusion is rife. A knowledgeable source who asked not to be identified says cattle that were healthy when they left a Texas farm appear to have brought the virus to a North Carolina farm. That raises the possibility that many cattle are infected but asymptomatic, which would make the virus harder to contain. Evidence suggests it has spread from cattle back to poultry, USDA says. Another source told Sciencenone that birds tested positive for the 3.13 strain and were culled at a Minnesota turkey farm right next to a dairy farm that refused to test its cattle. The industry and veterinarians bear some responsibility for the confusion, Lowe says. “We didn’t even try to get ahead of this thing,” he says. “That’s a black mark on the industry and on the profession.” Webby also faults USDA for not releasing data more quickly. The agency made six sequences from cattle—plus six related ones from birds and one from a skunk—available on the GISAID database on 29 March, 1 week after learning that cows were infected. It released one more sequence on 5 April, but then shared nothing else until the data dump 16 days later. Webby suspects the agency has moved cautiously because of the potential impact on the dairy industry. “There are a lot of people who are vested in this, and their livelihoods, at least on paper, can be impacted by whatever is found.”

Thijs Kuiken, an avian influenza researcher at Erasmus Medical Center, says the “very sparse” information released by the U.S. government has international implications, too. State and federal animal health authorities have “abundant information … that [has] not been made public, but would be informative for health professionals and scientists” in the United States and abroad, he says, “to be able to better assess the outbreak and take measures, both for animal health and for human health.” He notes that even the new sequences released by USDA do not include locations of the samples or the date they were taken. USDA said in a statement to Sciencenone that it will continue “to provide timely and accurate updates” and that its staff “are working around the clock” on a thorough epidemiological investigation to determine routes of transmission and help control spread. With its Sunday evening release, USDA made the unusual move to bypass GISAID—which requires a login and restricts how data can be used—and instead posted on a database run by the National Institutes of Health that everyone can access and do with as they please. USDA explained it did this “in the interest of public transparency and ensuring the scientific community has access to this information as quickly as possible to encourage disease research.”  The dairy industry is particularly worried that sales could suffer because of unwarranted fears that milk might infect people with the virus. The Food and Drug Administration (FDA) has said it has “no concern” that pasteurized milk presents risks because the process “has continually proven to inactivate bacteria and viruses, like influenza, in milk.”

But Lowe says for this specific virus, there are no data to back that claim. That’s “shocking,” he says. “It should not be that hard to get that data. I do not know why the foot dragging is occurring there.”

In a statement to Sciencenone, FDA said the agency is working to “reinforce our current assessment that the commercial milk supply is safe” and will share data as soon as possible. “U.S. government partners are working with all deliberate speed on a wide range of studies looking at milk along all stages of production, including on the farm, during processing and on shelves,” the statement said.

Daniel Perez, an influenza researcher at the University of Georgia, is doing his own test tube study of pasteurization of milk spiked with a different avian influenza virus. The fragile lipid envelope surrounding influenza viruses should make them vulnerable, he says. Still, he wonders whether the commonly used “high temperature, short time” pasteurization, which heats milk to about 72°C for 15 or 20 seconds, is enough to inactivate all the virus in a sample. Lowe predicts that with increased safety precautions at farms, including more rigorous cleaning of milking equipment, and the end to the seasonal movement of cattle, this outbreak likely will die out—as often happens when bird influenza viruses infect mammals that do not make particularly good hosts. But he and other researchers say to truly assess the continuing threat of H5N1 in cattle, they need to understand how this virus succeeded at infecting dairy cows in the first place. “Which cells is the virus replicating in? How is it getting around the body? What receptor is it using to get into cells?” Lowe wonders. “Those are the really interesting questions.”

Correction, 23 April 2024, 7:35 a.m.: A previous version of this story said James Lowe necropsied infected cows. He didn't but noted that researchers at Iowa State University did.

Hopes of a new weapon against diseases that routinely ravage colonies that are relied upon for food pollination. The world’s first vaccine for honeybees has been approved for use by the US government, raising hopes of a new weapon against diseases that routinely ravage colonies that are relied upon for food pollination. The US Department of Agriculture (USDA) has granted a conditional license for a vaccine created by Dalan Animal Health, a US biotech company, to help protect honeybees from American foulbrood disease. “Our vaccine is a breakthrough in protecting honeybees,” said Annette Kleiser, chief executive of Dalan Animal Health. “We are ready to change how we care for insects, impacting food production on a global scale.” The vaccine, which will initially be available to commercial beekeepers, aims to curb foulbrood, a serious disease caused by the bacterium Paenibacillus larvae that can weaken and kill hives. There is currently no cure for the disease, which in parts of the US has been found in a quarter of hives, requiring beekeepers to destroy and burn any infected colonies and administer antibiotics to prevent further spread. “It’s something that beekeepers can easily recognize because it reduces the larvae to this brown goo that has a rancid stink to it,” said Keith Delaplane, an entomologist at the University of Georgia, which has partnered with Dalan for the vaccine’s development.

The vaccine works by incorporating some of the bacteria into the royal jelly fed by worker bees to the queen, which then ingests it and gains some of the vaccine in the ovaries. The developing bee larvae then have immunity to foulbrood as they hatch, with studies by Dalan suggesting this will reduce death rates from the disease. “In a perfect scenario, the queens could be fed a cocktail within a queen candy – the soft, pasty sugar that queen bees eat while in transit,” Delaplane said. “Queen breeders could advertise ‘fully vaccinated queens.’” American foulbrood originated in the US, and has since spread around the world. Dalan said the breakthrough could be used to find vaccines for other bee-related diseases, such as the European version of foulbrood. As they have been commercialized, transported and pressed into agricultural service, honeybees have been exposed to a cocktail of different diseases that typically lay waste to large numbers of colonies and require major interventions by beekeepers to keep numbers up. The US is unusually dependent upon managed honeybee colonies to prop up its food pollination, with hives routinely trucked across the country to propagate everything from almonds to blueberries. This is because many wild bee species are in alarming decline, due to habitat loss, pesticide use and the climate crisis, fueling concerns around a global crisis in insect numbers that threatens ecosystems and human food security and health.