Dairy cattle movement networks govern the spread and persistence of H5N1 B3.13 in the United States

Avian influenza virus H5N1 is predominantly found in wild and domestic birds. H5N1 genotype B3.13 was first detected in United States dairy cattle in March 2024 and spread through much of the country during 2024 and 2025, resulting in the largest known H5N1 outbreak in domestic mammals. By analysing viral genomic data jointly with historical cattle movement patterns, we find that live cattle movement is the predominant contributor to H5N1 spatial spread, rather than wild or domestic birds. Using phylogeographic methods we estimate that >40% of interstate viral transmissions occurred before B3.13's first detection and >70% occurred before interstate dairy cattle movement restrictions were implemented in April 2024. After this implementation, interstate transmission slowed but within-state spread persisted, driven by local cattle network density and movement volume. Our epidemic simulations demonstrate that the connectivity of counties within and around the Texas Panhandle - where the earliest cases were documented - predisposed the region to become an outbreak epicentre. Counterfactual simulations indicate that interstate restrictions needed to have begun 2-3 months earlier in order to limit the epizootic substantively, given the extent of cryptic spread before detection. Network-informed interventions outperformed geographically-defined containment, but response speed (rather than intervention strength) was the limiting factor in our epidemic models, underscoring the need for surveillance systems capable of detecting pathogen emergence before widespread dissemination.

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Publication Details

Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2026-10-31
DOI
https://doi.org/10.64898/2026.10.28.762465
Primary Topic
Influenza Virus Research Studies
Type
preprint
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preprint

Dairy cattle movement networks govern the spread and persistence of H5N1 B3.13 in the United States

Ethan Plunkett, Gytis Dudas, Michael Worobey, Justin Bahl et al.
bioRxiv (Cold Spring Harbor Laboratory)
Influenza Virus Research Studies
preprint

Dairy cattle movement networks govern the spread and persistence of H5N1 B3.13 in the United States

Ethan Plunkett, Gytis Dudas, Michael Worobey, Justin Bahl, Prathyush Sambaturu, Thomas P. Peacock, Kristian G. Andersen, Martha I. Nelson, Adriaan M. Dokter, Michael W. Sanderson, Marc A. Suchard, Moritz U. G. Kraemer, Praneeth Gangavarapu, Guy Baele, Jonathan E. Pekar, Joel O. Wertheim, Karthik Gangavarapu, Andrew Rambaut, Alvin Crespo-Bellido, Yucai Shao, Jennine Ochoa, Tanin Rajamand, Philippe Lemey, Alexander Maksiaev, Oliver Pybus
preprint en

Abstract

Avian influenza virus H5N1 is predominantly found in wild and domestic birds. H5N1 genotype B3.13 was first detected in United States dairy cattle in March 2024 and spread through much of the country during 2024 and 2025, resulting in the largest known H5N1 outbreak in domestic mammals. By analysing viral genomic data jointly with historical cattle movement patterns, we find that live cattle movement is the predominant contributor to H5N1 spatial spread, rather than wild or domestic birds. Using phylogeographic methods we estimate that >40% of interstate viral transmissions occurred before B3.13's first detection and >70% occurred before interstate dairy cattle movement restrictions were implemented in April 2024. After this implementation, interstate transmission slowed but within-state spread persisted, driven by local cattle network density and movement volume. Our epidemic simulations demonstrate that the connectivity of counties within and around the Texas Panhandle - where the earliest cases were documented - predisposed the region to become an outbreak epicentre. Counterfactual simulations indicate that interstate restrictions needed to have begun 2-3 months earlier in order to limit the epizootic substantively, given the extent of cryptic spread before detection. Network-informed interventions outperformed geographically-defined containment, but response speed (rather than intervention strength) was the limiting factor in our epidemic models, underscoring the need for surveillance systems capable of detecting pathogen emergence before widespread dissemination.

bioRxiv (Cold Spring Harbor Laboratory)
Scripps Research Institute (US), The Pirbright Institute (GB), Royal Veterinary College (GB), University of Arizona (US), University of California, Los Angeles (US), University of Georgia (US), Vilnius University (LT), Kansas State University (US), Cornell University (US), Rega Institute for Medical Research (BE), University of Massachusetts Amherst (US), United States National Library of Medicine (US), University of California San Diego (US), University of Oxford (GB), Science Oxford (GB), Cornell Lab of Ornithology (US), Imperial College London (GB), University of California, Davis (US), University of Edinburgh (GB), KU Leuven (BE)
Influenza Virus Research Studies
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