by Bird flu was likely circulating in dairy cows at least four months before it was confirmed to be the highly pathogenic H5N1 virus, according to a new analysis of genomic data by scientists at the US Department of Agriculture’s Center for Animal Diseases.
The research also found infected cattle with no apparent links, suggesting “affected herds that have not yet been identified,” the study said.
It adds to a growing pile of evidence suggesting the H5N1 virus was prevalent in the US dairy industry for months before it came to the attention of scientists and government regulators.
The USDA study was published as a preprint, before peer review, on the BioRXIV server on Wednesday.
It follows a similar analysis by an independent international group of nearly two dozen evolutionary and molecular biologists who quickly analyzed raw genome sequences uploaded by the government to a server maintained by the National Library of Medicine. Despite the lack of critical background information on those samples, that group reached almost the same conclusion as the USDA: that the virus crossed from wild birds to cows between mid-November and mid-January, meaning that it had been circulating for months. before anyone knew.
The USDA officially confirmed the presence of the H5N1 virus on March 25 in a dairy cow in Texas. Since then, at least three dozen infected herds have been reported across nine states. At least one farm worker in contact with infected cows in Texas has tested positive for H5N1, the second human case of this type of flu ever reported in the US. The worker was given anti-viral medication and has recovered.
Tests of milk from retail stores showed inert remnants of the virus in about 1 in 5 samples, the US Food and Drug Administration reported last week, suggesting the infection had become widespread. Further testing by the FDA confirmed that the virus in the samples of pasteurized dairy products was not active and could not make anyone sick, but experts strongly advised against consuming raw milk.
“We could do a much better job” of catching H5N1 in dairy cows, said Dr. Michael Worobey, head of the Department of Ecology and Evolutionary Biology at the University of Arizona was part of the group of biologists who did the independent analysis. Worobey studies how pandemics start.
Worobey said that as soon as the cows were significantly ill with something mysterious, instead of testing for specific viruses and bacteria, ideally, a laboratory would use a technique called metagenomic sequencing, which reads the genetic material all in an example and using the help of computers. Pick out relevant information.
“Had that been done, H5N1 would have been introduced in January and then even after that,” he said.
If we’re serious about preventing outbreaks in animals that could lead to human pandemics, Worobey said, regulators need to change their approach.
“We have to get out of the mindset of waiting for attention to be paid to the tip of the iceberg of sick animals or sick people.” Instead, he said, animals must be routinely tested with “modern techniques” to identify emerging pathogens.
The new study gives the USDA’s account of how bird flu spread so quickly to flocks across the US. Samples collected between March 7 and April 8 found highly similar H5N1 viruses in 26 flocks in eight states and six poultry flocks in three states, suggesting the virus crossed in a single shedding event between wild birds and cattle. .
The study states that “production veterinarians” first noticed changes in milk production and milk quality in cows that were not eating well in late January.
H5N1 has been devastating wild and domestic bird populations in the United States since 2022, and has infected an increasing number of mammals.
As well as movement between cattle and wild birds, the study found evidence that infected cattle passed the virus to poultry flocks “through multiple transmission routes”. The researchers also discovered that a wild animal – a raccoon – and cats living near the cows on dairy farms were infected with the virus associated with the current outbreak.
Interestingly, there were key differences between the virus sequenced from the infected farm worker and the cow genome. The USDA scientists concluded that the differences could mean they were missing samples from the animals the farm worker came into contact with or could be due to the evolution of the virus from host to host.
Worobey says the study means H5N1 “now appears to be well within the country’s dairy cattle population” and may be something we have to deal with in the coming years.
While it’s not at all clear that this virus will evolve into the right mix of ways to launch a human pandemic, he said, allowing a virus to gain a foothold in a domesticated animal population puts everyone at risk.
“It adds one more species – a very important species – where influenza A virus has not previously circulated to the list of species where these viruses have the opportunity to find that right mix that allows them to wreak havoc in the human population, not only animals,” he said.
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