A Miserable Week as H5N1 Rolls on in Dairy, Poultry, and People
California remains the epicenter, but other states and poultry join the fray
As the California outbreak intensifies and Fall rolls on, H5N1 influenza seems to be making its forecast mark on the U.S. livestock and poultry industry. Official USDA counts can be found at the following site with links to poultry, livestock, mammals, and wild birds: 2022–2024 Detections of Highly Pathogenic Avian Influenza (usda.gov)
In summary California’s dairy case count now stands at 124 herds, with Michigan also adding a case this past week. Ominously, Utah and Washington reported outbreaks in 2 large layer flocks (2.69 million birds between them), both located in counties with major dairy populations. Neither state has publicly stated the clade of the H5N1 virus affecting the flocks, nor announced any plans at this point to test dairy herd bulk tank samples near the affected herds. Washington also announced a smaller infected poultry flock in a marine-adjacent area, perhaps related to wild bird populations.
The weekly CDC influenza overview, including the latest on the California human cases is found here: CDC A(H5N1) Bird Flu Response Update October 18, 2024 | Bird Flu | CDC
Public health officials in California and CDC on Friday announced that 13 workers on 11 infected dairy farms have now been confirmed positive with non-complicated cases of H5N1, with no evidence of onward transmission to date. This brings total confirmed infected individuals in the U.S. to 27 since the start of the outbreak.
For those interested in a more technical look at the phylogeny of the H, N, and PB2 sequences of the U.S. H5N1 isolates related to this outbreak in cattle, poultry and humans, data reported to GISAID as of 10/18 is here: GISAID - Highly Pathogenic Avian Influenza Outbreak in the United States
Just a reminder that many of the USDA-submitted sequences lack significant metadata due to privacy concerns, so it is difficult to say with certainty which states are associated with which isolates. However, past practice has been for USDA to publish sequences early from farms associated with human cases for CDC comparison. Here is a screenshot of a portion of the HA segment with the human cases marked and the “California Clade” labelled on the GISAID tree, assuming the recently deposited USDA isolates are from California farms matching the 6 deposited CDC human isolates:
Although there has been some speculation that the California outbreak in dairy cattle has been “more severe”, and the isolated viruses do contain some further single nucleotide polymorphisms (SNP’s) in multiple gene segments, no one has yet made claims for any of those changes being associated with known virulence factors in either cattle or humans. More detailed clinical metadata and research is required to associate genomic changes with enhanced disease outcomes. We still lack centralized capture of even basic disease outbreak data in dairy herds. APHIS Veterinary Services has not provided any plans for systematically collecting and analyzing such information from cooperating state animal health agencies. Concerns about increased severity remain observational, speculative, and ad hoc.
California is the largest state, both for humans and dairy cattle:
When people or cows in California get a potentially zoonotic infection, America notices! Two articles of note hit the press this week I’d like to highlight, both from highly reputable sources. The first came in the political newsletter POLITICO:
Avian Flu Spreading In California Raises Pandemic Threat To Humans - POLITICO
One paragraph in particular caught my eye:
But between March 31 and Oct. 14, only 25 individuals in the state have been tested for avian flu, according to CDPH. Workers who are symptomatic are first screened for flu before additional bird-flu-specific testing is performed. California is home to over 17,500 dairy workers, most of whom are in the Central Valley.
With 11 confirmed positive samples through October 14th, that means that 11 of 25, or over 40% of workers tested for H5 were positive! With over 17,500 workers and perhaps 10-15% of the herds now likely confirmed infected, the state has massively undertested an exposed population of maybe 2000 workers on those farms! Public health officials are only sampling a small percentage of likely infected dairy farm workers. That is not necessarily an untenable surveillance situation if aggressive back-up screening is in place at clinics and emergency rooms to diagnose and treat patients with more severe illness. However, the pool of at-risk individuals is huge; effective public health education and prevention programs for this group are a monumental challenge beyond the scope of my commentary.
The other point I’d make that was raised in this article is the risk for viral reassortment between seasonal H1N1/H3N2 human influenza viruses and H5N1:
This risk is higher in unvaccinated dairy workers incubating seasonal flu while exposed to H5N1 at work. An unlikely event during the summer outbreaks becomes much more plausible in the coming months as seasonal influenza activity accelerates. Most reassorted viruses are competitive failures in their host populations; however, one or more reassortants could theoretically take hold in people, cows, or even other species (e.g. swine, poultry).
A second article was authored by my most respected zoonotic-pandemic veteran reporter, Helen Branswell in STAT: Is it time to freak out about bird flu?
I found her closing remarks extremely wise:
So I have no answer for the question: How much worrying should we be doing about H5N1 right now? But I take some solace from the fact that flu experts don’t either.
The world’s leading flu scientists recently met in Brisbane, Australia, for a key flu conference that is held once every two years, Options for the Control of Influenza. As you might expect, there was a lot of discussion — some on the program, some in the hallways — of the H5N1 outbreak in U.S. dairy cattle. But even there, among the best minds on influenza in the world, there was no clarity about the risk the situation poses, said Malik Peiris, chair of virology at the University of Hong Kong’s School of Public Health.
Peiris has been studying this virus since it first triggered human infections in 1997 in Hong Kong. He has a very healthy respect for its disruptive capacities. No one Peiris heard or spoke to suggested that H5N1 could never gain the ability to transmit easily from person-to-person. But likewise, no one appeared confident that widespread human-to-human transmission of this virus is inevitable or even highly likely, he said.
There was agreement, however, around at least one notion: Letting this virus continue to spread unchecked in cows is profoundly unwise.
We really have not developed consistent policies or methods to reliably measure spread in the U.S. cattle industry, let alone check it. We have little or no data on the longer-term infection status of recovered herds or even individual recovered animals. Reinfected herds, if they occur, may not present the same prominent clinical features seen in naive infected herds, making recognition less straightforward (and easier to ignore). The U.S. is flying blind regarding both H5N1 2.3.4.4b B3.13 viral prevalence and genomic variations over time in both naive and previously infected herds. Perhaps it’s time to reprioritize our H5N1 viral surveillance in dairy cattle and milk towards broader objectives than voluntary dairy-driven regulatory and economic considerations.
We can pasteurize milk to maintain food safety; positive bulk tank statuses should not be an impediment for ongoing milk sales (except for retail raw milk producers).
1) Local herd milk viral genomic changes;
2) Targeting of worker safety protection and community surveillance; and
3) Cross species (poultry) and wildlife monitoring
are critical public and animal health objectives transcending the interests of dairy stakeholders currently blocking more universal bulk tank H5N1 monitoring proposals.
An HHS-FDA led routine mandatory bulk tank sampling and reporting program for milk itself might be initiated under FDA authority for regulating interstate movement of milk. This would leave intra- and interstate animal health issues aside for USDA and state animal health officials to address separately, based on known farm H5N1 milk-test status established through public FDA-required screening. I have no inside knowledge on whether such a scheme is legal or feasible. FDA regulates milk health and wholesomeness standards for interstate movement. The current H5N1 interagency approach has made USDA the lead agency in the effort, with their live animal regulations and limitations driving compliance questions. Under this approach HHS-FDA would take the lead, potentially allowing greater authority for requiring additional H5N1 testing of existing bulk tank samples for interstate movement of milk.
Ultimately, resolution of the H5N1 conundrum comes down to 2 factors yet to be determined:
Will H5N1 2.3.4.4b 3.13B continue to behave badly at an increasingly rapid pace? I can’t estimate a “tipping point”, but it’s certainly closer than it was a few weeks or months ago, and the rate of decay is increasing. We have the MO serology results and a whole raft of other human-based studies to digest. Additionally, California is adding human / cow cases at an alarming rate, and poultry outbreaks are a sleeping giant, with wildlife and cats as ever-present threats for headlines.
We’re now 16 days away from the election; barring a zoonotic catastrophe, no policy changes will occur before November 5th. After that, all bets are off, depending on the course of events and results of the election. The parties have wide differences in approach towards public health and relative cost-benefit ratios for actions against pandemic threats. The winning approach may well soon begin to play out in our H5N1 saga.
As my dear father always told me: “Wait and see…”
John