20 H5 Commercial Flock Infections in September, but Nobody Can Share a Genotype...
The NVSL Confirmatory Lab system for information "privacy" is killing advancements in understanding beyond an overworked regulatory community
Once again, updated research and new information is piling up faster than I can review it and intelligently comment on it for your review. I came away from the Leman Conference more convinced than ever that we are missing the boat with influenza in 2 very important ways:
The virus is exploding and transmitting within and between herds preclinically or at the onset of clinical disease; all of our diagnostic and intervention strategies are late and ineffective, i.e. closing the barn door after the horse has escaped. Ironically, some of the best evidence I heard is generated through human zoonotic infections of known negative pigs! It’s very challenging for high health swine farms to diagnose preclinical human viral influenza shedding in time to prevent viral spillover to naive swine contacts. More to come on that presentation from the Leman Conference. However, we have repeatedly seen the same phenomenon of preclinical viral shedding in both incubating poultry and dairy herds. This has huge implications for slowing both further farm and zoonotic spread by earlier diagnosis of infected farms, which is extremely difficult without pre-clinical screening of high risk farms prior to clinical disease symptoms.
Individual virus genotypes vary greatly in their minimal infectious dose, shedding levels presented to the host, and viral pathogenicity, which are in turn dependent upon their level of species adaptation, the immune environment of the host population, and environmental conditions. It’s intuitively obvious that the current clade(s) of H5N1 2.3.4.4b being presented by wildlife to our domestic poultry populations are quite capable spillover candidate(s), likely even more so than in recent years, given the levels of early season outbreaks.
Here is the current case list in the U.S., as of September 30:
It’s remarkable that we have suffered 20 commercial flock infections in 5 states in September, at least a month ahead of the typical start of the higher risk period for avian influenza transmission from migrating birds.
Additionally, USDA-APHIS has documented 342 HPAI detections in wild birds (mostly ducks) in the last 30 days, ending on September 30th:
What do we publicly know about the genotype or genotypes of this virus (or viruses) now overrunning us once again? The USDA has offered no detailed information regarding any of the isolates. I reached out to the state veterinarian offices in Wisconsin and Utah seeking more information on genotypes for those 2 recent outbreaks, given that both occurred in counties also housing significant numbers of dairy cows (also the case in some of the South Dakota counties). Presence of area dairy herds at least raises the (unlikely) possibility that the poultry infections could have originated as dairy herd spillovers.
I was pleased that both states promptly responded, stating that neither state had been informed of the genotype of the virus isolated from their flocks. I’m a retired 20+ year USDA-APHIS-Veterinary Services employee; I have no doubt that NVSL has not provided the affected states with written and curated phylogenetic results at this point. But I am also confident that experienced lab staff at NVSL know with a high degree of certainty the sequence genotypes within 24 hours or less of results coming off the sequencers. That information has undoubtedly been shared internally with APHIS leadership and the outbreak response infrastructure, including state participants. Regardless, it is long time policy and courtesy that states in general defer to NVSL’s information release policies for providing sequence information on isolates, while NVSL maintains that any earlier disclosures will be at the discretion of state animal health officials and/or APHIS leadership- circular buck passing! The elephant on the couch is that genotype data, paired with even state level locational and temporal tags can lead to potential trade and state-area disease status challenges or embarrassment for individual commodities or industries. [For example a B3.13 poultry strain in a NMTS negative state would indicate a likely infected dairy herd that had been missed and should be investigated.] Our regulatory system has developed complex graduated information release processes as data has become more powerful, negating much of the power that new molecular tools bring in understanding disease epidemiology and risk.
I checked in with expert sources who monitor the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) for USDA submissions. In summary, there are only 5 submitted but undated domestic chicken or turkey sequences from the last month of USDA SRA submissions (with 25 confirmed cases in late August-September). They are all D1.1 with no state or date of confirmation, per USDA policy, and may not even originate from the August-September sample sets. However, in wild birds (ducks), there is possibly a novel H5N1 2.3.4.4b reassortant appearing with a new matrix protein (MP) seen in several non-curated summer submissions that could potentially spill over into poultry; that will become apparent in due time. Additionally, NVSL is behind in their stated 6-week goal in curating SRA reads for submissions to GenBank-GISAID, with hundreds of noncurated SRA submissions from January to April of 2025. It’s safe to assume that these metrics will further deteriorate with the Federal Service now shut down.
I started this paper with the intention to advocate for more timely sharing of publicly obtained isolate information in the interest of more rapid and collaborative progress in addressing today’s H5N1, an obvious primary animal health and zoonotic threat. Then I watched/listened to most of the closing discussions held Tuesday during the National Science Foundation’s 2-day session on PPE. I was especially moved by comments from 2 producer-related participants. First, Anja Raudabaugh, CEO of Western United Dairies in California, vividly described the clinical realities of dealing with “endemic H5N1” in the face of day-to-day management of California dairy herds. The outbreak is not over in California, and recovering herds are not returning to a totally viral negative status. Adding naive “springers” to saemi-recovered herds is a fraught process, for the heifers! Their PPE issues partially revolve around when and where on the farm to deploy it with fluctuating endemic viral loads.
Then Oscar Garrison, Senior VP of Food Safety and Regulatory Affairs for United Egg Producers provided a very frank assessment regarding the current lack of understanding of the predominant epidemiological factors related to H5N1 entry and spread within poultry (layer) flocks. The newly recognized roles that aerosol or area viral spread from wild bird populations, dairies, neighboring poultry operations may play in moving infections needs a lot of research and assessment in addition to long-studied fomite contact threats.
I thought about the real life challenges these two producer representatives brought to the discussion; I then reflected on the “help” being provided by our regulatory bodies. The problems extend well beyond balky delayed data sharing:
How does a foreign animal disease (FAD) designation in poultry and select agent status for H5N1, now an endemic disease in wildlife, help anyone? It strangles our testing flexibility, enhances fear of reporting in many species, and impedes research. Are the well-worn sets of rules we live under with the “HPAI in poultry” paradigm really designed to make life better for anyone, or do they just perpetuate a 20th century bankrupted regulatory process that no longer works?
APHIS-VS currently has a regulatory monopoly on outbreak epidemiological and phylogenetic data; yet these are the 2 areas where producers are crying out for more specialized real-time expertise! Lombard, Melody et al in California made breakthrough discoveries on H5N1 dairy herd pathogenesis along-side outbreak response, not because of it! Our regulatory response work is not asking the right questions or getting on the farms soon enough, prior to clinical illness, to really understand outbreak epidemiology. Public reports summarizing findings and recommendations from multiple epidemiological investigations are not being generated. Available data is not being systematically collected and published by understaffed labs, response teams, and analysts!
Producers, local vets, and university epidemiological specialists should be proactively recruited in high-risk areas to observe as cases unfold, not just relying on VS-generated non-controlled post-outbreak case studies assessing pre-ordained fomite threats. Sharing the results of area phylogenetic data analysis in contemporary multi-site outbreaks is absolutely critical as well.
What right does USDA have to disallow proven efficacious vaccine use in multiple segments of the livestock industry in order to theoretically “protect” the economic interests of other segments? The broiler poultry industry should be able to certify freedom from vaccine use or alternatively, certify freedom from viral antigen in their product for trade, which is the real issue at hand! They perhaps should also certify antigen freedom for domestic consumers, given the recent incidence of infectious H5N1 virus allegedly found in a few batches of FSIS-inspected raw poultry-based pet foods.
To further complicate matters, as of today our Federal Government is shut down, and subject to further contractions in federal services:
Trump’s Grand Plan for a Government Shutdown - The Atlantic
In a memo last week, Vought, the OMB director, instructed federal agencies to prepare for significant “reduction-in-force” notices, or RIFs, to eliminate employees and projects that are not in line with Trump’s priorities. Some in the president’s orbit are encouraging him to take a hard-line stance. White House aides and allies believe that they will have the advantage as Washington careens toward tomorrow’s deadline. Some believe that a shutdown would give Trump fresh authority to fire civil servants en masse, including those who have been on paid administrative leave for months due to court rulings that prevented their termination…
Federal workers have become almost an afterthought and ultimately could become collateral damage in a lopsided partisan standoff, says Abby André, the executive director of the Impact Project, which has been tracking the fates of federal workers during Trump’s second term.
“Games of chicken are really common in the lead-up to shutdowns,” she told me. “But this administration has demonstrated a willingness to follow through on threats that previous administrations would have thought ill-advised for any number of reasons—chief among them having a functioning federal government.”
The lesson many Trump-administration officials have taken from eight months of paying federal workers to stay at home is that many functions of the government can be eliminated without massive public backlash. Most of Voice of America’s programming, for example, was shut down after Trump signed an executive order in March calling for the U.S. Agency for Global Media to be eliminated.
Patsy Widakuswara, the White House bureau chief for VOA, is among hundreds of journalists who have been on paid administrative leave since then. She is leading a lawsuit to get her job back and force VOA to restart operations in much of the world. But many of the broadcaster’s workers, who now face imminent risk of being terminated, are “paralyzed by fear” that Trump could close an agency that has been in place since World War II, she told us. Collecting her salary as a GS-14 employee—which amounts to $142,000 to $185,000 a year—while not being allowed to cover the Trump administration’s actions has been demoralizing, she said.
“I feel terrible as a VOA journalist, and I also feel horrified as an American taxpayer, because this is all waste,” she said. “The intention is not to improve anything. The intention is to just dismantle.”
Bringing these shifting governance developments back to this discussion, I think is it safe to assume that USDA-APHIS will be hard pressed to maintain current support for HPAI-related threats as we head into a likely extremely busy poultry outbreak season. Other mammalian and potential human outbreak risks this season are yet to be determined - remember, we don’t have any data on the genotype or latest SNP’s showing up in the poultry isolates to assess likely mammalian crossover potential.
I see no evidence that a shell-shocked USDA work force will undertake any new initiatives to improve HPAI response policies, especially given current leadership within the public health component of the federal government (RFK, Jr.). H5N1 vaccine policy changes seem roadblocked by political obstacles at this point. Much may depend on how badly B3.13 rebounds, if at all, in dairy herds, leading to new B3.13 poultry outbreaks. Additionally, wild bird-generated layer outbreaks could again become so widespread that high egg prices would force a policy change, too late to unscramble the mess.
The most critical question in my mind is how we’ll break the information (data) constraints on H5N1 infections to allow our capable scientific community to make faster progress on the current issues that vex multiple livestock industries. I’d personally advocate for creatively “going around” official regulatory live animal official testing requirements by utilizing non-official testing technologies, e.g. POC tests of various types, LAMP, etc. followed by whole genome sequencing (WGS), on non-individual animal samples (air, surfaces, retail milk and meat, oral fluids, nasal wipes, environmental, etc.). The immediate need is to obtain a range of H5N1 sequences with species, temporal and a degree of locational data over time and space, without directly testing case-defined live animals which fall under regulatory statute. This data should immediately go into the public domain as shared information. Over time anchored phylogenetic data will form based on non-direct sampling, providing more clues related to the unanchored USDA species sequence data. The entire phylogenetic dataset will gain value related to marking the significance of mutations in cross species spillover and clues for increased pathogenicity in mammals, for example.
This type of approach will require some initial non-traditional funding and guerilla leadership, given that the current system is heavily invested in official testing and traditional reporting confidentialities. These indirect sampling approaches have been tough sells in competitive funding proposals from government-based sources. However, I’m confident that with time and positive practical research results from enhanced studies, stakeholder demand for the next steps will drive further transparency in sharing data to improve animal and human health. The other scenario that would drive a rapid acceleration of anchored data would be a highly infectious human H5N1 outbreak, where human cases and associated animal isolates would serve the same function, not a comforting alternative.
What I saw yesterday in closing stakeholder comments (with one exception) was a building consensus and actually a surging demand for bold action to address H5N1 as it exists, rather than as we have traditionally planned for it. Those are 2 widely varying approaches that we are just beginning to unpack in domestic livestock production. The PPE discussions were just a subset of the bigger questions bedeviling the industries and stakeholders regarding how to handle this virus.
This is now a ubiquitous, mutable, reservoir virus in both avian and mammalian species displaying a significant preclinical shedding period in domestic livestock that makes traditional case definition-based laboratory sample diagnosis dangerously slow in concentrated animal feeding operations (CAFO’s). Both wildlife and area livestock production exposure are significant risks for further spread of the infection to naive herds/flocks. People that live and work with their livestock are coming to these realizations a lot faster than the state and federal authorities attempting to administer a static foreign animal disease eradication and control program that is no longer “fit for purpose”.
The current crisis in federal-state governance and support for research functions may provide an opportunity in disguise for visionary leadership to forge new regulatory processes to transparently protect animals, their owners/caretakers, and the public at the speed of commerce. Producers can all play ball and stay safe with H5N1, but the price to play will be radical transparency related to viral status for their farms, animals, and employees. Faster, better, cheaper has come to surveillance, diagnostics, treatment, and recovery for a host of disease threats, including H5N1. Producers and regulators better wholeheartedly embrace both speed and openness if we want to prosper.
John