The H5N1 bird flu virus began circulating in cattle in Texas in December

AAs agricultural officials and epidemiologists try to get their arms around the latest confusing chapter in the decades-long story of the H5N1 avian influenza virus — which has flowed into U.S. dairy cows — they are drenched in the virus’s genetic breadcrumbs. Leaves in the nose, lungs and, primarily, milk of animals.

On Wednesday, US Department of Agriculture scientists published A preprint – a study that has not yet been peer-reviewed – describes for the first time what their studies of 220 viral genomes from infected cows have done so far. The study’s authors report that the outbreak in cattle began from a spillover event from birds in the Texas Panhandle in early December. The USDA did not confirm the presence of H5N1 in the Texas herd until March 25.

“These data support a single introduction event to livestock from a virus of wild avian origin, possibly following a limited local circulation of approximately 4 months prior to confirmation by the USDA,” the authors wrote.

The findings add more precision to what has been previously reported by academic scientists. Studying viral genomes can provide clues to the outbreak’s origins and allow researchers to track how the virus, which primarily affects wild and domesticated birds, changes as it gets a foothold in cattle hosts.

A preliminary analysis of USDA genome sequence data released last week revealed by academic DNA sleuths that the outbreak in dairy cows has been going on for months longer than previously realized and may be more widespread than official numbers suggest. So far, 36 herds in nine states have tested positive for the virus, the USDA said.

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The new analysis also provides a window into how bird flu changes as it spends time in the body of livestock.

In the past few years, H5N1 has spread from wild birds to various carnivorous mammals, including foxes, bears and seals, but in each of those cases, the virus has died out. The outbreak in dairy cows is one of the first times this bird flu virus has been demonstrated to be able to spread efficiently between mammals, said virologist Thomas Mettenleiter, director of the Friedrich Loeffler Institute, a leading animal disease research center in Germany. From 1996 till his resignation last year. Another event was multiple outbreaks at mink farms in Spain and Finland in 2022 and 2023, respectively.

“These spillover events don’t usually lead to exchange chains,” he said. “This situation is definitely an eye-opener for me.”

The USDA’s analysis found about two dozen mutations that appeared in the H5N1 virus as it circulated in dairy cows, making influenza viruses more dangerous or more likely to infect humans.

“It’s very difficult to draw a risk map from that, but there seems to be a constant evolution,” Mettenleiter said. “It’s not surprising, but good to know. All of these mammal-to-mammal passages, as we do experimentally, put an evolutionary pressure on the virus, and that’s what we’re seeing with the increase in these known mammalian adaptation markers.

Vivian Dugan, director of the influenza division at the Centers for Disease Control and Prevention, told STAT Thursday that the mutations detected so far do not immediately raise red flags to pose a high risk to human health.

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“I think based on our analysis based on consensus and some [sequence] “The data — because we have a good data-sharing relationship with the USDA — we don’t see anything about us for mammalian adaptation, at this point,” Dugan said.

The CDC is testing existing H5 vaccines in ferrets The vaccine appears to confer cross-protection against the virus from an infected man in Texas.

Scientists frustrated by the slow trickle of data from USDA’s investigations took to social media to hail the preprint as progress. “I’m very grateful to this research team for sharing this, although I hope they didn’t keep the data just to make sure they published it first,” said virologist Angela Rasmussen, who studies pathogens that jump from animals to people in vaccines and epidemiology. Institute of Disease at the University of Saskatchewan, Saskatoon, Canada, Published in X Thursday.

For weeks, the agency has faced criticism from scientists and epidemiologists for a lack of transparency and timely sharing of information about the outbreak, undermining efforts to track its progress. When the USDA finally uploaded a large portion of the pathogen’s genome sequences to a public database, researchers were eager to examine the sequences to determine whether the H5N1 virus was changing as it passed from cow to cow. Include the necessary information about when and where the samples were collected. All are simply labeled “USA” and “2024”.

The USDA has refused to take that basic information — called metadata — out of the sequence files. The agency’s Animal and Plant Health Research Service has said it will quickly share raw sequence data until it becomes available and plans to upload “consensus sequences” when they are ready, when they are more fully edited and contain the metadata scientists are looking for.

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Helen Branswell contributed reporting.

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