#19,260
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.
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 reviewAbstract
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.
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.
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.
