The US is entering a riskier season for spread of H5N1 bird flu. Here’s why experts are worried

With the approach of fall and cooler weather across the United States, officials say the risk posed by the H5N1 bird flu virus could rise — and they’re taking steps to prevent the creation of a hybrid flu virus that could more easily infect humans.

Fall and winter months present more opportunities for H5N1 to spread and change since both cows and other flu viruses will be on the move. While most human infections in the current outbreak have been mild and self-limiting, each new host gives the virus a chance to get better at infecting people.

“To be clear, we have no evidence so far that this virus can easily infect human beings or that it can spread between human beings easily in a sustained fashion,” said Dr. Jennifer Nuzzo, director of the Pandemic Center at the Brown University School of Public Health. “If it did have those abilities, we would be in a pandemic.

“The second we know that someone gave it to someone else relatively easily, that’s a new pandemic, and it will be around the globe, probably in a matter of weeks,” Nuzzo said at a seminar hosted by the Health Coverage Fellowship.

The concern comes as scientists are urgently trying to solve the mystery of how a person in Missouri who had no contact with animals became infected by a type of bird flu.

Few details have been released. The person had “significant underlying health conditions” that probably made them more susceptible to the infection, Dr. Nirav Shah, principal deputy director of the US Centers for Disease Control and Prevention, said Thursday.

The patient tested positive for the flu after being hospitalized August 22, was treated with antiviral medications and has since recovered and returned home.

Additional testing by the Missouri State Public Health Laboratory confirmed that the person had a type of H5 flu, which is an uncommon subtype. Only 13 other H5 infections have been reported in humans in the US this year. Aside from the Missouri case, all have been in farm workers who had been in direct contact with infected birds or cows.

The CDC has confirmed that the Missouri case was an H5 infection and is now trying to sequence the rest of the virus’ genome to find out whether it is related to those infecting poultry and dairy cattle. It’s not clear whether the agency’s scientists will be successful, since there was little virus in the patient’s samples to work with. So far, CDC scientists had been able to sequence only part of the virus’ genetic material.

“The data that we do have and that have been generated thus far show an H5 virus that is closely related to the H5 virus circulating among dairy cows,” Shah said.

Investigators have also interviewed the patient and are tracing their recent contacts. There’s no indication that the person passed the infection to anyone else, and there’s no unusual flu activity in the area where the person lives, Shah said.

“Seeing that someone is in the hospital with possible H5N1 heightens my worry,” Nuzzo said. “It not only heightens my worry for the farm workers,” who are most at risk from infection, she said, “but it also heightens the worry that this we’re allowing this virus to gain new abilities.”

With herds on the move, risk increases

H5N1 caught scientists by surprise when an outbreak in US dairy cattle emerged in March. New cases slowed in the summer, when dairy cows move around less, partly due to heat and partly because demand for milk drops during the summer, when school is out, Dr. Eric Deeble, deputy undersecretary for marketing and regulatory programs at the US Department of Agriculture, said in August. But that starts to change in the fall, when farmers move cows so they can graze on the remnants of fields that have recently been harvested.

Greater movement of cattle could give the H5N1 virus more opportunities to spread.

“It is always of concern when folks are moving animals,” Deeble said.

The USDA has ordered the testing of dairy cows before they travel between states, but there’s no such requirement for cattle that are moving within the same state.

The order also doesn’t require the testing of every animal within large groups, and there’s concern that cows that are infected without symptoms may be moved undetected.

That concern was heightened after three dairy herds in California’s Central Valley tested positive for H5N1 last month. As of September 12, the total number of infected herds in California had jumped to eight, Deeble said Thursday.

California is home to about 1.7 million dairy cows, about one-sixth of the national total, making it the nation’s largest dairy producing state.

How and when the virus made its way to California is still under investigation. But genetic testing at the USDA’s National Veterinary Services Laboratories shows that the virus that infecting the California herds is very closely related to the viruses that have infected more than 200 herds from 13 other states, Deeble said.

The first infections of cows with the H5N1 virus were confirmed in herds in Texas and Kansas in late March. Evolutionary biologists think cows became infected months earlier, perhaps around the first of the year, when the virus probably spread from migrating birds who were carrying it.

The finding that the virus infecting the herds in California is genetically related to these first infections is important because it means they almost certainly are not the result of another crossover event from migrating birds to cows. Instead, the virus probably made its way to California through cow-to-cow spread that still hasn’t been controlled.

“So we were dealing essentially with one variant from the very beginning of this outbreak,” Deeble told CNN. “That information has been shared back with California, and so they’re continuing their epidemiological investigation with that knowledge in hand.”

Wastewater testing has been picking up H5 viruses in California since March 18, said Dr. Marlene Wolfe, assistant professor of environmental health at Emory University and program director for WastewaterScan, a monitoring network directed by researchers at Stanford and Emory universities and funded by the Sergey Brin Family Foundation.

California is one of nine states — of 40 being monitored in their network — where H5 viruses have been found in wastewater.

Wastewater testing can pick up viruses with the H5 proteins, but it can’t tell whether those viruses came from birds, cows, other animals or even discarded milk that had found its way into the sewage system. So far, though, most states that have had H5 proteins turn up in wastewater have also reported infected herds.

“So far, eight of these states have had outbreaks reported in cattle. The one state with an H5 detection that has not had an H5N1 cattle outbreak is Arkansas,” Wolfe wrote in an email.

Flu viruses can swap genes

The increased movement of animals will come as seasonal flu viruses are picking up steam in the US, increasing the likelihood that a person — probably a farmworker — could get infected with both bird flu and seasonal flu at the same time.

One of the most dramatic ways flu viruses can change is a phenomenon called reassortment.

Flu viruses are a little bit like Tinkertoys; they keep their genes in easy-to-detach segments. When two flu viruses infect the same cell and get close together, they can simply swap these segments and give rise to viruses that can sometimes have dramatic new properties.

A reassortment event that gives rise to a new souped-up flu virus is rare but not unheard-of. Reassortment of the flu viruses in pigs, which have similar flu receptors to humans, is believed to have given rise to the H1N1 virus that caused the 2009 pandemic, for example. Reassorted flu strains are also thought to have caused pandemics in 1957 and 1968.

Since 2010, the CDC has recommended annual flu vaccines for everyone 6 months of age and older. Still, less than half of all adults and children in the US got a flu shot last year, according to CDC data.

To try to prevent a reassortment event, flu vaccines will be particularly important for people who work directly with farm animals this year, the agency said.

The agency has asked states with infected herds to submit plans outlining how they will educate farm workers and deliver vaccines to those who want them. On Thursday, the CDC said it hoped to begin these intensive outreach efforts to farmworkers in October.

Increasing vaccination rates among farmworkers is going to be a tall order, said Bethany Alcauter, director of research and public health programs at the National Center for Farmworker Health.

“What we’ve been hearing everywhere is the number of farms and the number of dairy employees who are getting [personal protective equipment] and getting information, accurate information, about bird flu is really in the minority,” Alcauter said.

That’s true for a variety of reasons, she said, starting with farming culture. Some trades like construction require safety training. The same is not true of farming.

“Health and safety training in agriculture isn’t that common,” Alcauter said. Because many dairy operations are small, they aren’t usually covered by the government agency that oversees worker safety, the Occupational Safety and Health Administration, or OSHA.

Alcauter’s organization has been given about $4 million by the CDC to spread the word. She said it is taking applications from community groups and health centers to educate farmworkers about bird flu and encourage vaccination. She estimates that it will be able to fund 40 to 50 organizations.

Just like in any population, there will be some individuals who are hesitant about vaccination, but in general, she says, farmworkers tend to be accepting of vaccines because they often come from countries like Mexico and Guatemala that have large national vaccine campaigns.

Advocates for farmworkers say that while getting these workers vaccinated for seasonal flu viruses is a reasonable idea, those vaccines still don’t protect them from the viruses they could get from poultry or cows.

Though the government has ordered that nearly 5 million doses of H5N1 vaccine be packaged and made ready for use, there are no plans to actually give these doses to anyone, including farmworkers, who are most at risk.

This policy stands in contrast to Finland, which has seen past H5N1 outbreaks on fur farms. That country announced that it would begin vaccinating its farmworkers against H5N1 this summer.

Stopping the next pandemic

Adam Kucharski, a professor of infectious disease epidemiology at the London School of Hygiene & Tropical Medicine, says viruses that cause pandemics emerge in stages: They infect animals and establish a reservoir in stage one; these animals infections cause isolated spillover infections into humans in stage two; spillovers cause localized clusters of human infections in stage three; widespread transmission among people is stage four.

Kucharski argues that the most feasible and impactful stage for pandemic prevention is at stage two, when there are spillovers that cause localized clusters of infections. He says that the recent clusters of infections of farmworkers culling poultry in Colorado suggest that the H5N1 outbreak in the US is in that second stage, when prevention efforts can be less costly and more impactful.

“So really, it’s those situations where you’re starting to see evidence of ability to infect humans but not ability to sustain transmission very easily where there’s a prime potential for intervention,” Kucharski said.

But the US is not doing enough to take advantage of the H5N1s currently limited spread, he said.

Kucharski points to an outbreak of H7N9 in 2013 as a prime example of a situation where this worked. People were starting to catch this flu from live poultry markets in China, which shut down those markets and effectively stopped transmission of the virus.

“We haven’t had an H7N9 pandemic. We haven’t actually had many cases at all subsequently,” Kucharski said.

The US is running a risk letting H5N1 infections continue to spread in cattle without more widespread testing, and the world is watching.

“I think at the moment, the response doesn’t seem to be at the level it needs to be for this kind of threat,” Kucharski said.

“I think we saw, even in the early stages of Covid, that a lot of countries – lot of Europe, lot the US – basically wasn’t looking hard enough for Covid and then got caught out very badly when they realized that there was a lot more transmission than the raw data suggested,” Kucharski said.

“And so I think, particularly in this situation, getting a good grasp of what’s going on is kind of key, and I think we haven’t been getting that anywhere near the scale we need to.”

US to pay to develop bird flu tests

The CDC says the threat of the H5N1 virus is currently low. But federal agencies are taking steps to mitigate infections, should they begin to spread more widely.

The CDC said Thursday that it was awarding $5 million in funding to five commercial laboratories used by doctors and hospitals to develop tests to detect H5 viruses: Labcorp, Quest Diagnostics, Aegis Sciences Corporation, Ginkgo Bioworks and ARUP Laboratories. The agency is also looking to have these labs develop tests for Oropouche viruses, which are causing outbreaks in South America and Cuba.

In making the grants, Shah said, the agency was trying to learn from mistakes made during past public health emergencies.

“Previously … CDC developed tests for emerging pathogens and then shared those tests with others, and then after that, commercial labs would develop their own tests,” Shah said Thursday. “That process took time. Now with these new arrangements, commercial labs will be developing new tests for public health responses alongside CDC, not after CDC.”

CORRECTION: This story has been updated to note that the source of the funding for WastewaterScan is the Sergey Brin Family Foundation.