A new analysis of genomic data conducted by scientists at the US Department of Agriculture's Animal Disease Center suggests that bird flu, specifically the highly pathogenic H5N1 virus, was circulating in dairy cows for at least four months before it was officially confirmed. The research also revealed the presence of infected cattle with no apparent connections, indicating the existence of unidentified affected herds. These findings add to the growing body of evidence indicating that the H5N1 virus had infiltrated the US dairy industry long before it came to the attention of scientists and regulators.

The study, published as a preprint on the BioRXIV server, supports the conclusions drawn by an independent group of evolutionary and molecular biologists. This group, which analyzed raw genome sequences uploaded to the National Library of Medicine's server by the government, reached a similar conclusion to the USDA's research. Both studies suggest that the virus crossed over from wild birds to cows between mid-November and mid-January, indicating months of undetected circulation.

The confirmation of the H5N1 virus in dairy cows was officially announced by the USDA on March 25 in Texas. Since then, at least three dozen infected herds have been reported across nine states. Furthermore, one farmworker who had contact with infected cows also tested positive for H5N1, marking the second human case of this strain of avian flu in the US. Fortunately, the worker received antiviral medication and has since recovered.

Tests conducted by the US Food and Drug Administration (FDA) have shown remnants of the virus in approximately 1 in 5 samples of milk from retail stores, suggesting widespread infection. However, further testing by the FDA confirmed that the virus in these samples of pasteurized dairy products was inactive and posed no threat to human health. Nonetheless, experts strongly advise against consuming raw milk due to the potential risks associated with the virus.

Dr. Michael Worobey, a leading expert in pandemics from the University of Arizona, expressed concern over the missed opportunities to detect H5N1 in dairy cows earlier. He suggested that using metagenomic sequencing, a technique that reads all genetic material in a sample and utilizes computational tools to identify relevant information, could have revealed the presence of the virus as early as January.

To prevent future outbreaks in animals that could lead to human pandemics, Worobey emphasized the need for regulators to adopt a more proactive approach. Routine testing of animals using modern techniques for identifying emerging pathogens should be implemented, according to him.

The USDA's study sheds light on how bird flu rapidly spread to herds across the US. Samples collected between March 7 and April 8 revealed very similar strains of H5N1 in 26 herds across eight states and in six poultry flocks across three states, indicating that the virus likely originated from a single spillover event between wild birds and cows.

Moreover, the study found evidence of multiple transmission routes between infected cattle and domestic poultry flocks. The researchers also discovered that the virus had infected a wild animal, a raccoon, as well as cats living near the dairy farms.

Notably, the virus sequenced from the infected farmworker exhibited key differences from the cow genomes. The USDA scientists speculated that these differences could be attributed to missing samples from the animals the worker had contact with or to the evolution of the virus from host to host.

Worobey concluded that H5N1 seems to be firmly established in the US dairy cattle population and could pose a long-term challenge. While it is uncertain whether this virus will undergo the necessary changes to cause a human pandemic, allowing the virus to persist in domesticated animals exposes everyone to risk. The introduction of a new species, particularly one as significant as dairy cows, to the list of potential hosts for influenza A viruses raises concerns regarding the possibility of devastating consequences for both animals and humans.

In light of these findings, experts warn of the importance of vigilance and proactive measures to prevent the spread of bird flu and potential future pandemics.