Preprint: Within- and between-host dynamics of highly pathogenic avian influenza in domestic birds from Pennsylvania farms and live bird markets

Graphic Generated By Gemini using USDA Data
 

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Last month 3 east coast states (RI, NJ, PA) reported outbreaks of H5N1 in Live Bird Markets (LBMs), raising the tally to 14 markets across 5 states (New York, Pennsylvania, Florida, Rhode Island, and New Jersey) reporting outbreaks in 2026.

Going back 4 years we find 78 reports across 7 states (New York, Pennsylvania, Florida, Rhode Island, New Jersey, Virginia, and California). 

As mentioned 3 weeks ago in USDA Reports Another H5N1 Outbreak at a Live Bird Market (Pennsylvania) - despite 3 June outbreaks in LBMs - the USDA had reported  zero outbreaks in commercial poultry in the region in the previous 90 days. 

Last month, in One Health: Mapping reported modes of transmission of HPAI A (H5N1) to humans: A scoping review, we looked at how live bird markets have traditionally played a large role in the spread (and evolution) of avian flu viruses.  

Exposure to live birds from LBMs has often been cited as a major risk factor for human infection with avian flu - particularly in Asia -  and we've seen cases whose likely exposures were cited as simply living near, or walking past an LBM (see J. Infection: Aerosolized H5N6 At A Chinese LBM (Live Bird Market)).

All of which brings us to a new preprint, published this week, which examines how HPAI H5N1 spread and evolved inside poultry farms and live bird markets in Pennsylvania between 2023 and 2025.

Due to its length, I've only posted some excerpts. Follow the link to read it in its entirety.  I'll have more after the break.

Within- and between-host dynamics of highly pathogenic avian influenza in domestic birds from Pennsylvania farms and live bird markets

Anna S Jaeger, Elena Cruz-Adames, Stephen D Shank, Irina Chupikova, Katie Kumta, Eman Anis, Louise H Moncla
doi: https://doi.org/10.64898/2026.07.17.739193
This article is a preprint and has not been certified by peer review

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Abstract

Since late 2021, highly pathogenic avian influenza viruses (HPAI) of the H5 subtype clade 2.3.4.4b have spread across the Americas, devastating wildlife, agricultural animals, and resulting in dozens of human spillovers. National surveillance strategies generally provide only a single representative sequence per poultry outbreak, precluding fine-scale geographic transmission inference or studies of within-outbreak evolution. 

We produced high-quality deep sequence data from 46 infected Galliformes and Anseriformes sampled from commercial farm and live bird market (LBM) outbreaks in Pennsylvania from 2023-2025. We found that H5N1 viruses were introduced into Pennsylvania at least 68 independent times. 

We recover independent origins of live bird market outbreaks within the same county 3 weeks apart, and transmission between Pennsylvania LBM and New York commercial birds, suggesting high transmission risk within the Northeast live bird market distribution system. 

Analyses of within-farm variant populations show frequent variant sharing between samples from the same outbreak, suggesting that variants are propagated among epidemiologically linked infections. We identified 9 known adaptive mutations in these samples, including one instance of PB2 D701N in a LBM chicken sample, suggesting that while rare, concerning mammalian adaptive mutations can be present within these domestic outbreaks. 

Our data suggest that domestic bird outbreaks support high circulating diversity and wide transmission bottlenecks, increasing the risk of minority variants arising and propagating between infections. These data can help inform targeted biosecurity measures and better quantify the risk of viral adaptation during agricultural outbreaks.

       (SNIP)

We identified approximately 17 independent introductions into Pennsylvania that resulted in domestic infections. Most strikingly, we identify multiple distinct introductions into live bird markets in Pennsylvania among samples collected less than three weeks apart. Upon further phylogenetic analysis of transmission between Pennsylvania and New York, we present compelling evidence of transmission between live bird market settings and distributors in these states, as well as New Jersey. Live bird markets and their distribution systems are a high risk environment for transmission of HPAI given their diverse sources, mixed species, and historical lack of regulations and compliance to biosecurity measures [46,47]. 

More recently, particularly since the influx of HPAI in4 North America, stronger regulations and biosecurity measures have been implemented at the state level for live bird market systems, in particular by the Live Bird Marketing System Biosecurity Assurance Program [48]. 

Our finding of LBM transmission involving domestic birds from multiple states, along with ongoing detections in the LBMS suggest that additional interventions, improvements, or regulation may be needed.

(SNIP)

Taken together, we show here the first of its kind data from natural infections in domestic birds utilizing phylogenetic and within-host methods to quantify diversity, evolution, and transmission across domestic outbreaks. The multiple independent introductions into the state throughout the epizootic show that Pennsylvania is likely a representative model state for understanding finer-scale transmission dynamics of H5N1. 

Our results present evidence that high levels of diversity is being shared within domestic outbreaks, and particularly that continued surveillance and increased regulation of live bird market systems is important for controlling interstate spread particularly within the Northeastern United States. Future study and surveillance where samples are collected from individual domestic infections will allow for true quantification of transmission bottlenecks to further inform biosecurity and control measures in domestic settings. 

        (Continue . . . )

 

In 2016's Interventions in live poultry markets for the control of avian influenza: A systematic review Vittoria Offeddu , Benjamin J. Cowling, and J.S. Malik Peiris laid out the risks of avian influenza from live bird markets, reviewed some of the possible interventions, and concluded:

 

Highlights

• Avian influenza viruses (AIVs) can infect humans. Bird-to-human transmission is particularly intense in live poultry markets.
• Periodic rest days, overnight depopulation or sale bans of certain species significantly reduce AIV-circulation in the markets.
• Market closure would lastingly reduce the risk of animal and human infection.

While there have been numerous attempts to phase out LBMs (see 2009's China Announced Plans To Shut Down Live Poultry Markets In Many Cities), most have encountered stiff public resistance. 

Larger, more modern cities like Hong Kong have gone to great lengths to regulate and restrict live bird markets, and last year, Shanghai Banned Live Poultry Sales until at least 2027.

Currently the CDC considers the risk of human infection (at least, for the general public) from our current clade 2.3.4.4b strain of H5N1 to be low. LBMs are treated as a `manageable' risk; where rest days, mandatory testing, enhanced cleaning, and occasional short‑term shutdowns are employed rather than permanent closures.

But HPAI H5 is always evolving, as the recent introductions of the B3.13 and D1.1 H5N1 genotypes attest.  How long the risk from LBMs will remain manageable is anyone's guess. 

In the meantime, the author's of today's report suggest that - in view of the ongoing detection of avian flu in LBMs - `. . . additional interventions, improvements, or regulation may be needed'.

Queensland Reports `Presumed Positive' H5N1 Test in Migratory Seabird

 

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After going a week without any new reports of H5N1 in Australia or New Zealand, overnight Queensland's Department of Agriculture announced that samples from a deceased petrel found on Moreton Island (25 miles N.E. of Brisbane) have (preliminarily) tested positive for H5N1.

Initial testing was by the Queensland Government’s Biosecurity Sciences Laboratory (BSL). Samples have been forwarded to CSIRO’s Australian Centre for Disease Preparedness for confirmatory testing.

Typically, even when CSIRO has been unable to fully sequence a sample, Australia has been treating local test results as `likely positive'.  Two announcements from Queensland's government follows:

Queensland detects first case of H5 bird flu


The Department of Primary Industries is responding to a suspect positive case of H5 high pathogenicity avian influenza (H5 bird flu) in Queensland.

This is Queensland’s first suspect positive case of H5 bird flu in a wild seabird.

Samples from a deceased petrel found on Moreton Island have tested positive for H5 bird flu during initial testing at the Queensland Government’s Biosecurity Sciences Laboratory (BSL).

Samples have been sent to CSIRO’s Australian Centre for Disease Preparedness for confirmatory testing.

Australia’s first case of H5 bird flu was reported on 20 June in Western Australia, with further detections in wild seabirds in WA, SA and NSW.

There remain no detections in poultry, nor evidence of large-scale deaths in any animals in Queensland.

The community is being urged to continue to report sick or dead wild birds.

Department of Primary Industries Chief Veterinary Officer Allison Crook said the suspect positive detection was expected and Queensland is well prepared for the next steps.

“We have known that a H5 bird flu detection in Queensland was a matter of when, not if,” Dr Crook said.

“The Queensland Government is well prepared to respond. This suspect positive result has not impacted our poultry sector or domestic wildlife,” she said.

“We are continuing our enhanced passive surveillance program throughout the state and would encourage the community and industry to continue to be vigilant,” Dr Crook said.

“If you find sick or dead wild birds or wildlife, avoid contact, keep children and pets away, record what you see, and report immediately to the Emergency Animal Disease Hotline on 1800 675 888.”

Suspect positive case of H5 bird flu

Biosecurity Queensland has detected suspect positive H5 bird flu in a deceased wild migratory seabird found on Moreton Island (Mulgulpin).

This result is not unexpected following the recent detections of H5 bird flu in Western Australia, South Australia and New South Wales.
On this page

What we are doing
What you need to do
Actions for bird and livestock owners
Signs of bird flu in birds
More information

What we are doing

We are:

• continuing to carry out surveillance
• testing birds and animals
• working with industry, government agencies and response partners
• supporting strong biosecurity practices to help reduce the risk of spread
• keeping Queenslanders informed as the situation develops.

Queensland has been preparing for H5 bird flu and has strong response arrangements in place. Australia also has national arrangements to respond to animal disease incidents.

What you need to do

If you see sick or dead wild birds or wildlife:

• Avoid contact with sick or dead birds, wildlife and their environment. Do not touch or collect them.
• Record what you see, if it is safe. Record the number of dead or sick birds or animals, the species, location, date and time. Take a photo if you can.
• Report sick or dead birds or wildlife to the Emergency Animal Disease Hotline on 1800 675 888.

Your report will be reviewed, and we will contact you if more information is needed. Not all reports will require follow-up, sampling, or further action.

Actions for bird and livestock owners

If you own, care for or work with poultry, review your biosecurity practices now. A strong biosecurity plan helps protect your birds and your property.

Bird and livestock owners should report unusual signs of disease or sudden deaths immediately to the Emergency Animal Disease Hotline on 1800 675 888.

Poultry owners should:

• keep poultry away from wild birds
• keep feed and water where wild birds cannot access it
• keep sheds, yards, aviaries and equipment clean
• limit visitors to areas where birds are kept
• ask essential visitors if they have recently been on other properties with poultry
• wash hands before and after handling birds and eggs
• change into clean footwear before entering poultry areas
• keep good records of bird movements or sales
• report unusual signs of disease or increased deaths in birds.
• Signs of bird flu in birds

Signs can include:

• sudden death
• lack of coordination, tremors or swimming in circles
• twisted necks or other unusual posture
• inability to stand or fly
• diarrhoea
• difficulty breathing, coughing or sneezing
• swelling around the head, neck and eyes
• cloudiness or change in colour of the eyes.

More information

Stay up to date with the H5 bird flu current situation in Queensland.
Visit birdflu.gov.au for more information.

Probably Nothing . . . But It feels a Bit Like Deja Flu

 
Credit China Daily - March 2006

#19,258

Readers with extremely long memories will remember the great shuttlecock shortage of 2006, which was blamed - at least partially - on China's reported culling of roughly 200 million birds between 2003-2006 due to HPAI H5N1. 

This was back when China actually acknowledged avian flu outbreaks in their poultry or wild birds, something which rarely happens today.  The most recent FAO avian flu activity map (since Oct 1st 2025) shows almost no HPAI H5 in Mainland China. 

Of course, South Korea and Japan both saw major avian flu outbreaks, and in South Korea they are still dealing with a serious egg shortage due to the culling of 11 million birds last winter. 

While it seems reasonable to assume that China (and Russia) both saw some poultry losses from avian flu last winter, you wouldn't know it from their official reports. 

All of which brings us to a Yonhap News report overnight which reads almost beat-for-beat like the 2006 article posted above.  So much so, I had to double check to make sure it wasn't a phantom news report from the past.

Badminton Shuttlecock Prices in Japan Soar... Shortage of Chinese Duck and Goose Feathers

Posted July 23, 2026, 15:30

They report a `stagnant demand for duck meat', which they attribute to `changing Chinese diary habits', which has resulted in a growing shortage of duck and goose feathers, and is forcing a move towards using `synthetic shuttlecocks'. 

While this article provides few details, it does state: 

`However, as avian influenza (AI) has recently been rampant, disease control costs have increased due to concerns about infection, worsening the management of poultry farms and leading to a shortage of feathers, a raw material.' 

Perhaps the most important caveat is, although this article mentions avian influenza as a potential factor, that doesn't necessarily mean HPAI H5.  China continues to battle multiple avian viruses, including LPAI H9N2, H3Nx, H6Nx, and H10Nx viruses. Some recent blogs include:

Virulence: Surveillance and biological characterization of H3 subtype avian influenza viruses in Eastern China

J. Inf.: Zoonotic Threat of Novel H6N2 Avian Influenza Virus with Internal Genes Exclusively Derived from H9N2, China, 2025

Vet. Microbiology: The novel H10N3 Avian Influenza Virus Acquired Airborne Transmission Among Chickens: An Increasing Threat to Public Health

Admittedly, this reported shortage of duck feathers is a weak signal at best, but the paucity of official reports from China makes it worth our notice, since we've seen other similarly vague news items prove to be significant in the past.

In 2008 a report by Helen Branswell (then of the Canadian Press) described an early signal of the first SARS-CoV outbreak in 2002. She reported:

Surging vinegar sales in China grabbed the attention of the folks who regularly scour the globe for what might be budding disease outbreaks, like those who work for the Canadian-led Global Public Health Intelligence Network. 

"We were getting lots of rumours, like a lot of sales of vinegar," explains Dick Thompson, who was the spokesperson for the World Health Organization's communicable diseases section at the time.

“Vinegar in southern China is used as a disinfectant. And so if there’s a run on vinegar, there’d be a suspicion that there was some kind of infectious disease or a widespread belief that there is an infectious disease outbreak. So at these meetings we’d been hearing this kind of drip, drip, drip come in about that.”

While our visibility of avian flu in China is limited, it is worth noting that last November - in China MOA Announces New Guidelines to Expedite Animal Vaccine Strain Approvals - we saw a rare acknowledgement that their agricultural vaccines program (including avian flu) was in need of an overhaul. 

Whether today's report turns out to be significant remains to be seen. Like I said, it is probably nothing. 

But, it does seem curious enough to warrant a mention.

China CDC Weekly: First Human Infection with Influenza A(H1N2)v Virus — Yunnan Province, China, 2026

 

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While avian flu continues to sit at - or near the top of - most people's pandemic threat lists, swine influenza viruses (which often spread stealthily in pigs) may pose similar risks.  

Unlike many avian flu, swine variant viruses are already well adapted to a mammalian host, and in many ways porcine physiology is remarkably similar to that of humans (see The pig: a model for human infectious diseases).

Swine flu viruses are primarily H1 and H3 subtypes; both of which have a long track record of sparking human pandemics (see Are Influenza Pandemic Viruses Members Of An Exclusive Club?).

Since 2010 we've seen more than 500 scattered reports of human infection with swine variant influenza viruses (H1N1v, H1N2v & H3N2v) in the United States, often associated with agricultural exhibits at county and state fairs.   

Many of the viruses circulating in pigs today are descendants of human flu viruses which spilled over into swine over the years. This sharing of viruses is a two-way street. 

The CDC's IRAT (Influenza Risk Assessment Tool) lists 3 North American swine viruses as having at least some pandemic potential (2 added in 2019).

H1N2 variant [A/California/62/2018]  Jul   2019   5.8  5.7 Moderate

H3N2 variant [A/Ohio/13/2017]          Jul   2019   6.6  5.8 Moderate

H3N2 variant [A/Indiana/08/2011]      Dec 2012   6.0  4.5 Moderate

In addition to the 3 North American swine-variant viruses on the CDC's IRAT list, we continue to watch the evolution of China's EA H1N1 `G4' virus, Brazil's H1N2v virus, and emerging variants (and spillovers) in Europe (see ANSES Reports A `New' Swine Flu Virus Has Taken Over Other Genotypes in France).

But most of the world only rarely bothers to test, or to share reports on, swine influenza.

Last April, in WHO Influenza at the human-animal interface (March 31st): 13 Novel Flu Infections Detailed, we saw a very busy WHO report which included two brief accounts from Yunnan Province, China on an H1N1v and an H1N2v human infection.

Swine influenza viruses in humans

Influenza A(H1N1)v, China

On 20 March 2026, China notified WHO of a laboratory-confirmed case of A(H1N1)v influenza virus infection in a child from Yunnan province. The patient had onset of illness on 30 January 2026, was hospitalized on 2 February with pneumonia, and recovered in a few days. The patient had reported exposure to domestic pigs prior to illness onset.

Influenza A(H1N2)v, China 

On 3 February 2026, China notified WHO of a laboratory-confirmed case of A(H1N2)v influenza virus infection in a child from Yunnan province. The patient had onset of mild illness on 20 January 2026, and the infection was laboratory-confirmed on 2 February 2026. The patient had reported exposure to domestic pigs prior to illness onset. This case and the one above are not epidemiologically linked.

While both follow the typical pattern of recent exposure to pigs, last week the CCDC published a more detailed review of the H1N2v case which walks back that initial assertion. Instead, they now report:

Notably, unlike many previously reported A(H1N2)v cases in which direct exposure to swine was identified as a key risk factor (8), no direct contact with poultry or livestock was reported in this patient. This finding suggests that indirect or environmental exposure may play a role in the development of infection. 

This isn't the first time we've seen swine variant influenza infection in humans without recent contact with pigs (see here, here, and here), but it is a noteworthy finding. 

Due to its length, I've only posted some excerpts from the CCDC report. Follow the link to read it in its entirety.

Outbreak Reports
First Human Infection with Influenza A(H1N2)v Virus — Yunnan Province, China, 2026
Lihua Chen1, 2, Yaoyao Chen3, Xiaoyu Han3, Ruize Ni3, Ming Zeng4, Jie Deng4, Chunyuan Deng5, Guijing Chen5, Xiaoqing Fu3, Jibo He1, Chunrui Luo3,  

Summary

What is already known about this topic? 
Human infections with influenza A(H1N2)v viruses of swine origin have been sporadically reported in several countries, usually following direct or indirect exposure to pigs or contaminated environments. However, sustained human-to-human transmission has not yet been documented.

What is added by this report? 
This report describes the first laboratory-confirmed human infection with the influenza A(H1N2)v virus in China. Whole-genome sequencing showed that all eight gene segments were closely related to influenza viruses of swine origin circulating in China. No secondary human cases were identified among the close contacts, and no evidence of sustained human-to-human transmission was detected.

What are the implications for public health practice? 
This highlights the importance of routine influenza-like illness surveillance, timely whole-genome sequencing, and systematic investigation of unusual influenza A infections. Strengthened surveillance at the human-animal interface and cross-sector collaboration under the One Health framework are essential for early detection and risk assessment of variant influenza viruses.

(SNIP) 

DISCUSSION

This investigation documented the first confirmed human infection with the influenza A(H1N2)v virus in China. Similar to previous reports from the United States and Europe, human infections with A(H1N2)v have remained rare and have primarily been associated with influenza A viruses of swine origin that cross the species barrier (6). Most reported cases present with mild-to-moderate influenza-like illness, and sustained human-to-human transmission has not been documented (7). The clinical presentation in the present case was consistent with these observations, further supporting the characterization of A(H1N2)v as a sporadic zoonotic pathogen with limited transmissibility. The key finding of this investigation is that a swine-origin influenza A(H1N2)v virus was detected in a young child through routine ILI surveillance, with whole-genome sequencing supporting a swine-origin reassortant virus and no evidence of secondary human transmission.

Notably, unlike many previously reported A(H1N2)v cases in which direct exposure to swine was identified as a key risk factor (8), no direct contact with poultry or livestock was reported in this patient. This finding suggests that indirect or environmental exposure may play a role in the development of infection. Environmental contamination, shared living spaces, and short-distance exposure to animal housing have been proposed as alternative transmission pathways for various influenza viruses, particularly in rural settings where humans and animals coexist in close proximity (9).

These findings underscore the complexity of exposure assessment in zoonotic influenza investigations. In the present case, pigs and poultry were raised near the residence, and influenza A virus was detected at low viral loads in several pig and environmental samples. These findings support the possibility of indirect environmental exposure, but do not prove the exact source of infection.

(SNIP)

Human infection with the influenza A(H1N2)v virus described in this investigation represents a sporadic zoonotic event with no evidence of onward transmission and a limited public health impact. This case is comparable to previously reported A(H1N2)v infections globally, which are characterized by mild illness and the absence of sustained human-to-human spread.

Nevertheless, this finding highlights the ongoing risk posed by variant influenza viruses at the human–animal interface. Strengthened sentinel surveillance, timely epidemiological investigation, enhanced laboratory capacity, and cross-sector collaboration under the One Health framework remain critical for the early detection and mitigation of potential future outbreaks, confirming that human A(H1N2)v infection in China provides important evidence for national influenza surveillance and emphasizes the need to strengthen the genomic monitoring of swine-origin influenza viruses.

        (Continue . . . )

It is worth noting that this patient was seen by local clinics 3 times before finally being admitted to a hospital where lab tests confirmed H1N2v 10 days after the child's illness began. 

Mild-to-moderate influenza rarely results in testing for novel flu subtypes, which often only occurs if a patient is hospitalized.  As a result, we've no idea how many cases fly under the surveillance radar. 

While most of the emerging novel viruses we look at in this blog will probably never pose a genuine global health threat - there are a lot of contenders out there - and it only takes one overachiever to make an indelible mark on the world. 

Preprint: HPAI H5N5 in a Polar Bear and Atlantic Walrus, Svalbard, 2026, with Widespread Seroconversion in Polar Bears

 

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While running a distant 2nd to H5N1, a spin-off ressortant - HPAI H5N5 - continues to make inroads in northern Europe, Canada, and the United States (see March 2026's Viral Creep: H5N5 Update), and in the fall of 2025 it fatally infected a backyard poultry keeper in Washington State.

Four years ago the Norwegian Veterinary Institute reported both H5N1 and H5N5 for the first time in wild birds on Svalbard, which lies above the Arctic circle (see More HPAI (H5N5 & H5N1) Detected In Arctic (Svalbard).

Since then we've been tracking a small - but growing - number of spillovers of H5N5 to mammals in both Europe and Canada, including seals in the UK, domestic cats in Iceland, and raccoons (and other small mammals) in Canada.

Credit: Multiple transatlantic incursions of HPAI

clade 2.3.4.4b A(H5N5) virus into North America and spillover to mammals 

Two summers ago (2024) in Cell Reports: Multiple Transatlantic Incursions of HPAI clade 2.3.4.4b A(H5N5) Virus into North America and Spillover to Mammals, researchers reported finding the mammalian adaptive E627K mutation in a number of samples. 

Note: Many of the H5N5 viruses that have spread across Canada and the United States have reassorted with local LPAI viruses, and are now genetically distinct from the Svalbard & European lineages, making direct comparisons difficult. 

Two months ago (May 20th) the Norway Veterinary Institute, announced the detection of HPAI H5N5 virus in both a dead walrus and a polar bear on Svalbard Island. 

Although no other animals were confirmed infected during this investigation, there were eye witness accounts of two other polar bears exhibiting potential neurological symptoms. 

Today we've an unusually rapid follow-up report; a preprint published yesterday on the bioRxiv server that reports that H5N5 exposure is far more common among polar bears on Svalbard island than previously thought.

Somewhat surprisingly, most polar bears appear to survive H5N5 infection, although severe (and likely neurotropic) illness can occur.  

First, the Abstract and a few excerpts from the preprint, but you'll want to read it in its entirety. I'll return after the break with a bit more. 

Highly Pathogenic Avian Influenza H5N5 in a Polar Bear and Atlantic Walrus, Svalbard, 2026, with Widespread Seroconversion in Polar Bears
 Knut Madslien,  Johanna Hol Fosse,  Jon Aars,  Cathrine Arnason Bøe, Magnus Andersen,  Kayla Buhler, Ingvild Fjeldheim,  Britt Gjerset, Torhild Jørgensen,  Ida Kristin Myhrvold,  Andreas Rohringer,  Kjersti Sturød,  Morten Tryland,  Bjørnar Ytrehus, Ragnhild Tønnessen,  Ingebjørg Helena Nymo
doi: https://doi.org/10.64898/2026.07.20.739480
This article is a preprint and has not been certified by peer review [what does this mean?].
  
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Abstract

Highly pathogenic avian influenza virus (HPAIV) subtype H5N5 was detected in a one-year-old polar bear (Ursus maritimus) and an adjacent adult Atlantic walrus (Odobenus rosmarus rosmarus), both found deceased in Raudfjorden, Svalbard. This represents the first confirmed case of HPAI in a European polar bear and the second in an Atlantic walrus.

Viral genomes were nearly identical and harbored PB2-E627V, a marker associated with mammalian adaptation. Several polar bears, including the deceased individual, had previously been observed feeding on the walrus carcass. 

Antibodies against H5 were detected in 75% of polar bears in 2023 (n=36) and 97% in 2024-2025 (n=65), suggesting extensive circulation of HPAIV in the population following the first detections in birds in Svalbard in 2022, whereas no antibodies were detected in samples from 2014-2022 (n=243).

        (SNIP)

Although no human cases have been linked to the HPAIV H5N5 PB2-E627V cluster, its detection across diverse mammalian species indicates a broad host range. Occurrence in both terrestrial and marine mammals suggests that ecological interactions, including predation and scavenging, may facilitate cross-species transmission.

These findings are consistent with incremental, multigenic adaptation enabling infection of multiple hosts without evidence of full mammalian adaptation. Although HPAIV H5N5 can be zoonotic (43), the risk of zoonotic spillover to humans is considered very low for H5N5 detected in wildlife species with little or no human contact.

Nevertheless, the transmission to novel host species underscores the importance of timely risk assessment, surveillance, and infection preparedness, as well as awareness and adherence to appropriate biosafety measures among wildlife professionals.

Continued circulation within an avian-associated lineage as well as uncertainties on disease reservoir and adaptation underscores the need for disease surveillance at the wildlife–human interface in Arctic and North Atlantic regions.

The current report highlights that H5 HPAIV circulates in Arctic ecosystems and infects apex predators. Although no population-level effects are currently evident, detection in brain tissue and field observations suggest that disease can occur at the individual level. The identification of PB2-E627V and additional polymerase-associated changes is consistent with adaptation to mammals within an avian-associated lineage. These findings highlight the need for continued surveillance to clarify transmission pathways, evolutionary dynamics, and potential health effects.

        (Continue . . . )

Whether H5N5 has `legs', and can compete successfully against a far more  prevalent H5N1 virus, remains to be seen. But its persistence, and continued evolution, make it very much worth watching. 

Perhaps the bigger question is how much `silent' transmission of HPAI H5Nx is occurring unnoticed in mammalian wildlife?

The above preprint lists only one confirmed infection of a polar bear with H5N5 on Svalbard island, yet seroprevalence studies suggest 97% exposure.

How common this kind of disparity might be in other species is unknown. 

Surveillance here in the United States - and around the world - is mostly passive, and based on the successful detection, recovery, and testing of dead animals found in the wild. 

The USDA only lists 813 mammalian wildlife detections in the United States over the past 4 years, which likely only represents a tiny fraction of actual infections. 

There are a few studies which suggests much greater infectivity, including last year's Serological Evidence of Exposure to Eurasian-Lineage HPAI H5N1 Clade 2.3.4.4b in Wild Mammals in Ohio, USA, 2024-2025, which found substantial evidence among trapped raccoons and opossums from Ohio marshes where H5N1 had already been confirmed in waterfowl. 

They reported:

Specifically, antibodies to avian influenza virus nucleoprotein were detected in 54.9% (n = 61) of samples using enzyme-linked immunosorbent assay; antibodies to Eurasian-lineage highly pathogenic avian influenza H5 clade 2.3.4.4b and North American low pathogenic avian influenza H5 were detected in 43.2% (n = 48) and 22.5% (n = 25) of samples, respectively, using virus neutralization assays; and antibodies to avian influenza virus neuraminidase were detected in 44.1% (n = 49) of samples using enzyme-linked lectin assay. 

Yet officially, Ohio has only detected 5 instances of H5N1 (4 domestic cats, 1 mink), and none in mammalian wildlife.  

While all of this is admittedly based on just two surveys - involving different subtypes and different mammalian species - this reminds us that much of what H5Nx is doing in the wild occurs outside of our view.  

While ignorance may be bliss, what we don't know can come back and hurt us. 

 

Preprint: Bovine-derived H5N1 influenza virus efficiently infects lactating swine via the mammary gland

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As alarming as the spillover of HPAI H5N1 to dairy cattle has been, the mammalian livestock species believed to have the greatest potential for spawning new reassortant viruses is swine, which are known to harbor a wide variety of influenza A viruses.  

Although detections in swine have been limited, we've seen scattered evidence that H5N1 can infect pigs, albeit often asymptomatically. A few past reports include:

• WHO H5N1 detected in pigs in China (2004)
• EID Journal: Asymptomatic H5N1 In Pigs (2010)
• An Unusual Report Of H5N1 in Pigs (Indonesia 2016)
• Sci. Rpts.: Evidence Of H5N1 Exposure In Domestic Pigs - Nigeria (2018)
• Study: Seroconversion of a Swine Herd in a Free-Range Rural Multi-Species Farm against HPAI H5N1 2.3.4.4b Clade Virus  (Italy, 2023).

In May of 2023, in Netherlands: Zoonoses Experts Council (DB-Z) Risk Assessment & Warning of Swine As `Mixing Vessels' For Avian Flu, we looked at growing concerns in Europe that avian H5N1 could increase its pandemic threat by spreading (and evolving) in farmed swine.

But the reality is, testing for avian flu viruses in pigs remains both voluntary and rare. According to the USDA, as of Sept.1, 2025 there were 74.5 million hogs and pigs on U.S. farms, but in their last published Influenza A Virus in Swine Surveillance report (Q4), they report testing only  977 samples in 2025.

The USDA further notes:

Due to the voluntary nature of this surveillance, the information in this report cannot be used to determine regional and/or national incidence, prevalence, or other epidemiological measures, but it may help identify IAV-S trends.

Since HPAI H5 often presents in pigs as a mild or even asymptomatic infection, and surveillance is generally passive, there are many opportunities for the virus to spread silently in swine herds. 

We've revisited this topic several times in recent weeks.  

Earlier this month, in J. Virology: Receptor profiling and growth assessment of influenza A virus in porcine mammary and non-mammary tissues and derived cells, we looked at an in vitro study that tested the infectivity and replication of 4 different influenza viruses (Bovine H5N1, LPAI H5N1, Swine H1N2, and Human H1N1) across an array of porcine cell lines (primary nasal turbinate, trachea, lung and mammary gland epithelial cells).

They reported that porcine mammary epithelial cells contain both SA-α2,3 avian‑type and SA-α2,6 human‑type receptor cells and can support replication of bovine H5N1 B3.13 to relatively high titers, suggesting lactating pigs are a plausible host for this genotype.

Four days ago, in EID Journal: Detection of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Genotype D1.2 Virus in Swine after Experimental Inoculation, we looked at live animal study that found that H5N1 genotype D1.2 appears to be well suited to mildly (or asymptomatically) infect - and replicate systemically - in pigs.

Today we can add a preprint (not yet peer-reviewed) from Ohio State University which finds that a bovine-derived D1.1 genotype (from a Nevada dairy herd) of H5N1 efficiently infects the mammary gland of lactating pigs, and that viral RNA  was detected in oral swabs of suckling pigs.

I've only posted the abstract, and a brief excerpt. Follow the link to read it in its entirety.  I'll have a brief postscript after the break.

Bovine-derived H5N1 influenza virus efficiently infects lactating swine via the mammary gland
 Min Liu,  Natalie N Chillson, Emma A Martin, Hannah J Cochran,  Janice Y Park, Brady O'Boyle,  Devra Huey, Kara N Corps,  Andrew S Bowman, Cody J Warren
doi: https://doi.org/10.64898/2026.07.18.739312
This article is a preprint and has not been certified by peer review [what does this mean?].

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Abstract

Since 2024, highly pathogenic influenza A(H5N1) viruses have spread extensively among U.S. dairy cattle, where they replicate efficiently in the mammary gland and are shed at high titers in milk. To directly assess susceptibility of commercial swine populations to bovine-derived H5N1 virus, lactating sows with prior influenza virus vaccination histories representative of U.S. commercial swine production systems were inoculated via the intramammary route and co-housed with their 1-week-old piglets to evaluate disease outcomes, viral replication, and potential for vertical transmission. 

Intramammary inoculation of lactating sows resulted in sustained viral RNA shedding in milk, while piglets exhibited sporadic oral viral RNA positivity that mirrored viral kinetics in milk. Lesions in mammary tissue and viral antigen staining, as well as development of neutralizing antibody responses and changes in milk color and consistency, further confirmed infection in the sows. 

Despite these molecular findings, none of the animals developed overt clinical disease, and respiratory involvement was not noted during the study period.

Collectively, we demonstrate that intramammary exposure results in productive influenza A(H5N1) virus infection in lactating sows despite their vaccination histories, indicating the potential threat of viral spillover into commercial swine populations. The clinically inapparent nature of infection presents a risk of subclinical spread and underscores the importance of expanding viral surveillance to swine.

       (SNIP)

Collectively, this study expands the host and tissue contexts in which contemporary influenza A(H5N1) viruses may threaten agricultural production and public health. The clinically inapparent presentation in sows suggests that observation for overt disease alone may be insufficient to detect infection in swine.

As a common limitation for large-animal studies conducted under BSL-3Ag containment, the small sample size (n = 4 sows) restricts our ability to evaluate animal-to-animal variability or perform robust dose-dependent comparisons.

However, similar patterns of viral RNA shedding, infectious virus recovery, and mammary tissue pathology, as well as viral RNA positivity in piglets, support the conclusion that lactating sows are susceptible to influenza A(H5N1) infection following intramammary exposure. 

Given the role of swine in IAV evolution and reassortment, early detection of influenza A(H5N1) infection in this host population should be a priority for animal and public health preparedness. 

(Continue . . . )

Despite the mounting evidence of the susceptibility of cattle, sheep, goats, and pigs to HPAI H5 - and the continued calls from the scientific community for more aggressive surveillance and testing of livestock (see here, here, here, here, and here) - the world seems content to don blinders and hope for the best.

A dubious strategy, but one that has the advantage of letting us put off the hard decisions until it is too late to do much about them.