Evidence map›Paper›PMID 41959054›Full record

ArticlebioRxiv : the preprint server for biology2026

The emergence and molecular evolution of H5N1 influenza viruses in United States dairy cattle.

Jonathan E Pekar, Karthik Gangavarapu, Alvin Crespo-Bellido, Thomas P Peacock, Joel O Wertheim, Gytis Dudas, Jeffrey B Joy, Meera Chand, Florence Débarre, Praneeth Gangavarapu and 16 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

26 authors.

Jonathan E PekarInstitute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.ORCID 0000-0003-0977-2886
Karthik GangavarapuDepartment of Translational Medicine, The Scripps Research Institute, La Jolla, CA, USA.
Alvin Crespo-BellidoDivision of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892.
Thomas P PeacockThe Pirbright Institute, Woking, UK, GU24 0NF.
Joel O WertheimDepartment of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
Gytis DudasInstitute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Jeffrey B JoyBritish Columbia Centre for Excellence in HIV/AIDS.
Meera ChandUK Health Security Agency, London UK.
Florence DébarreInstitut d'Écologie et des Sciences de l'Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France.
Praneeth GangavarapuDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Daniel H GoldhillDepartment of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
Natalie GrovesUK Health Security Agency, London UK.
Xiang JiDepartment of Statistics, Iowa State University, Ames, IA 50011, USA.
Lorena Malpica SerranoDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85705, USA.
Louise MonclaDepartment of Pathobiology, University of Pennsylvania, PA 19104, USA.
Angela L RasmussenVaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada S8N 5E3.
Christopher RuisVPD Heart & Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK.
Divya VenkateshDepartment of Biology, University of Oxford, Oxford OX1 3SY, UK.
Moritz U G KraemerDepartment of Biology, University of Oxford, Oxford OX1 3SY, UK.
Oliver G PybusDepartment of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
Kristian G AndersenDepartment of Translational Medicine, The Scripps Research Institute, La Jolla, CA, USA.
Marc A SuchardDepartment of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Martha I NelsonDivision of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892.
Philippe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
Michael WorobeyDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85705, USA.
Andrew RambautInstitute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.

Funding

NIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00014 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI GARCIA-SASTRE, ADOLFO · 2021 to 2025
$62.6M
NIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00015 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HENSLEY, SCOTT · 2021 to 2025
$50.7M
Technology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Kristian Graugaard Andersen · 2018 to 2026
$32.0M
CHROME: Continuum of HIV Response through Observational Molecular EpidemiologyR01AI192139 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WERTHEIM, JOEL OKRENT · 2025 to 2025
$2.9M
Statistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4M
NIAID NIH HHS R01 AI153044NIAID NIH HHS R01 AI192139NIAID NIH HHS U19 AI135995NIH HHS 75N93021C00014NIH HHS 75N93021C00015Wellcome Trust
6 · The paper itself

Abstract

Prior to 2024, highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses circulated predominantly in wild birds and poultry. In 2024 and 2025, 2.3.4.4b genotypes B3.13 and D1.1 were detected in United States dairy cattle. Using whole-genome and segment-specific phylodynamic inference, we estimate that B3.13 and D1.1 spilled over from wild birds into dairy cattle in late 2023 and late 2024, respectively. Spillover occurred shortly after the formation of the reassortant genotypes and was followed by months of cryptic transmission prior to detection. We found that both B3.13 and D1.1 evolved at higher rates in cattle relative to birds, primarily due to relaxed purifying selection. Site-specific analyses identified genomic sites under positive selection in cattle relative to birds, indicating adaptation and likely contributing to improved viral fitness after spillover. Intensified genomic surveillance in dairy cattle is essential as population immunity introduces additional selection pressures, with ever-changing risk for human emergence.

Identifiers

PMID41959054
PMCPMC13060070

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.