Genetic study shows that the cow H5N1 flu virus outbreak most likely began earlier than previously believed
An analysis of genetic sequences released on Sunday by the U.S. Department of Agriculture suggests that the H5N1 bird flu outbreak in dairy cows in the United States has likely been ongoing for months longer than previously thought and has likely spread more widely across the nation than the confirmed outbreaks would imply.
The genomic data suggest a single spillover event that most likely happened in late 2023, University of Arizona evolutionary virologist Michael Worobey told STAT on Tuesday.
Along with many experts from the U.S. and Europe, Worobey worked on the analysis. "The bad news is it looks like this is well entrenched, has been in cattle for a long time, and... probably very, very, very widespread," Worobey said.
"If that's accurate, it has been going unnoticed for a really long, embarrassing, frustrating time," Worobey remarked. Furthermore, we are unaware of the full extent of its asymptomatic spread and its magnitude. Furthermore, we're attempting to address this issue well after the horse has run off.
According to him, the genetic sequence from the human case—which happened on an undisclosed Texas farm—is enough distinct from the sequences from the cattle to make a connection between them difficult. The variations point to two possible scenarios: either the person contracted the infection independently, maybe through contact with infected wild birds rather than a cow, or there may have once been a different virus line that attacked cattle but has since vanished.
What's known as metadata, or details such as the location of the sample collection site, the specific time of collection, and the section of the infected animal from which the sample was taken, was absent from the 239 genetic sequences that the USDA released on Sunday. The fact that they only say "USA" and "2024" restricts the ability of other scientists to interpret what they are witnessing.
When asked if he felt more aware of the threat H5N1 poses to humans as a result of the genetic data analysis, Worobey said he was uneasy about the fact that the virus appears to be spreading across mammals, describing it as unprecedented.
He proposed that, considering the degree of human contact to cattle, the outbreak warrants a more serious response than it has received thus far. "To begin with, we simply must study it thoroughly and try to bridge the knowledge gap between what is occurring and what is known."
The USDA didn't initially establish an H5N1 outbreak in dairy cows in Texas until late March, despite indications of an enigmatic disease afflicting the animals as early as February. The number of reported infections has increased to 33 herds across eight states since then. It has been determined that one individual—a farm worker who experienced conjunctivitis—was infected.
The USDA is unsure if there has been a single spillover occurrence when the virus was spread to cows by infected wild birds, or if these cases are all related and the consequence of workers, agricultural equipment, or cattle movement. It informed STAT last week that it could establish connections between the sick herds in Kansas, New Mexico, and Texas; additionally, it is known that the first infected Michigan herd discovered contained cows that had been imported from Texas. However, the USDA hasn't been able to distinguish those outbreaks from others that have occurred in South Dakota, Ohio, North Carolina, and Idaho.
According to Worobey, the genetic sequences cluster too tightly for this to represent anything more than a single overflow. "If it were repeatedly leaping from bird to cattle... I don't think you would just end up with the same extremely low genetic diversity, where every internal segment has the same pattern.
Those who watch the hazardous H5N1 virus are not comforted
by the possibility that an outbreak has been going on for longer than
previously believed.
Worobey's interpretation of the data was confirmed by Tom Peacock, an influenza virologist at the Pirbright Institute, a British organisation that focuses on managing viral diseases in animals.
In a prior report, the USDA stated that it thought a virus from an infected cattle herd had entered a nearby Michigan poultry business. According to Peacock, the genetic sequences supplied by the USDA for cows, poultry, and other afflicted species indicate that the hypothesis is accurate. "All cattle sequences, along with those of cats, chickens, grackles, and other animals, cluster when viewed collectively."
"The human case is the thing that doesn't fit that picture," he declared.
According to Peacock, "it's basically too distant a cousin to be directly connected to this outbreak, which either means there was an early bifurcation of the cattle sequences or it's a second spillover."
According to Peacock, it would have been useful to know if any of the sequences of cattle had been produced from samples obtained on the farm where the worker who was affected was believed to have come into contact with the virus. However, that data is not accessible.
Having the virus in a mammalian species that humans
frequently come into touch with provides H5N1 "more shots on goal,"
or more opportunities to acquire the mutations necessary for it to evolve and
become capable of infecting humans, according to Worobey. "That is not
good."