The outbreak of the H5N1 flu virus in cows probably started earlier than thought

TThe outbreak of H5N1 bird flu in dairy cows in the United States has likely been going on for months longer than previously thought and has likely spread more widely across the country than confirmed outbreaks would imply, according to an analysis of genetic sequences released Sunday by the US Department of Agriculture.

The genetic data points to a single spillover event that likely occurred in late 2023, Michael Worobey, an evolutionary virologist at the University of Arizona, told STAT on Tuesday.

“The bad news is that it looks like this is well established and has been in cattle for a long time and … is probably very, very, very widespread,” said Worobey, who worked on the analysis with a number of scientists in the US and Europe . .

He suggested the outbreak should be taken more seriously than has been the case so far, especially given the amount of exposure people have to livestock. “We need to study it thoroughly first … and see if we can close the gap on what’s happening and what we know.”

Although there were reports of a mysterious illness in dairy cows in Texas as early as February, the USDA first confirmed an outbreak of H5N1 in dairy cows in that state in late March. Since then, the number of confirmed outbreaks has risen to 33 herds in eight states. One person – a farm worker who developed conjunctivitis – has been confirmed to be infected.

The USDA is unclear on whether these outbreaks are all related — the result of the movement of livestock, farm equipment or workers — or if there have been multiple spillover events in which infected wild birds transmitted the virus to cows. Last week, STAT told STAT it could find links between infected herds in Texas, Kansas and New Mexico; It is also known that cows in the first infected herd discovered in Michigan were brought in from Texas. But USDA has been unable to draw a line between these outbreaks and others in Idaho, Ohio, North Carolina and South Dakota.

The genetic sequences cluster too close together to be anything other than a single spillover, Worobey said. “If it jumped from bird to cattle over and over again … I wouldn’t think you would get the same very limited genetic diversity with each of the internal segments showing the same pattern.”

The prospect of an outbreak that has been going on for months longer than previously known is not reassuring to those tracking the dangerous H5N1 virus.

“If that’s true, it’s been flying under the radar for an embarrassing and frustratingly long time,” Worobey said. “And we have no idea to what extent it is spreading asymptomatically and how widespread it is. And we try to deal with something long after the horse has run away.

Tom Peacock, a flu virologist at the Pirbright Institute, a British organization focused on controlling viral diseases in animals, agreed with Worobey’s reading of the data.

The USDA previously reported that it believed the virus had made its way from an infected herd of cattle to a nearby chicken farm in Michigan. The genetic sequences for cows, poultry and other infected species released by the USDA suggest the hypothesis is correct, Peacock said. “If you look at all the bovine sequences together, they all cluster, just like the cats and the chickens and the grackles and all that.”

“What doesn’t fit into that picture is the human case,” he said.

The genetic sequence of the human case, which occurred on an unidentified farm in Texas, is different enough from the cattle sequences that it cannot be easily linked to them, he said. The differences suggest that the individual was either infected during a separate event – ​​perhaps not from a cow, but through contact with infected wild birds – or that another lineage of viruses may have been present in cattle early on and has since become extinct.

“It’s actually too distant a cousin to be directly linked to this outbreak, meaning it’s either a second spillover or an early split of the bovine sequences occurred,” Peacock said.

The 239 genetic sequences the USDA shared Sunday do not contain so-called metadata: information about where the sample that generated the sequence was taken, what part of the infected animal’s body it was taken from, or when exactly the collection took place. They simply list “US” and “2024,” which limits how well outside scientists can interpret what they see.

Peacock said it would have been useful to know whether any of the bovine sequences were generated from samples taken at the farm where the infected worker was believed to have been exposed to the virus. But that information is not available.

When asked whether the analysis of the genetic data increased his sense of the risk H5N1 poses to humans, Worobey suggested he was uncomfortable knowing that H5N1 appears to be spreading among mammals, calling that unprecedented .

Having the virus in a mammalian species with which humans have frequent contact gives H5N1 more opportunities to acquire the mutations needed to evolve to infect humans, or “more shots on target,” Worobey said. “That is bad.”