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Peer-reviewedCC BY 4.0Transboundary and Emerging Diseases

Large‐Scale Genomic Surveillance of Swine Influenza A Viruses in Europe Highlights Increased Reassortment Potential and Field‐Based Associations With Clinical Manifestations

  • Kathrin Lillie-Jaschniski1
  • Zalán Homonnay2
  • Gwenaëlle Dauphin1
  • István Kiss2
  • Susanne Zoels3
  • Julia Stadler3
  • Nick Vereecke4,5
5 affiliations
  1. 1Ceva Animal Health, Libourne France
  2. 2Scientific Support and Investigation Unit Ceva-Phylaxia Campus Budapest Hungary
  3. 3Clinic for Swine Centre for Clinical Veterinary Medicine Ludwig-Maximilians-Universität München Oberschleissheim Germany uni-muenchen.de
  4. 4Laboratory of Virology Department of Translational Physiology Infectiology and Public Health Faculty of Veterinary Medicine Ghent University Merelbeke Belgium ugent.be
  5. 5PathoSense BV Lier Belgium
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Abstract

Swine influenza A virus (swIAV) is an important One Health pathogen due to its genetic diversity, ongoing reassortment, and implications for animal and public health. Between 2022 and 2023, nasal swabs (NSs) from pigs of multiple age groups were collected from 134 farms across 16 European countries and analyzed by real‐time quantitative PCR (RT‐qPCR), subtyping, and whole‐genome sequencing. Clinical and management metadata were integrated with viral genotypes. swIAV was detected in 93% of the targeted farms included in this study, with Clade 1A (H1pdmN1) and Clade 1C (H1avN1, H1avN2, and H1huN2) predominating. Sequencing identified 23 genotypes, including 12 previously unreported ones. Exploratory analysis suggested potential associations between specific hemagglutinin (HA) (sub)clades and clinical signs in piglets and with herd management factors. High genotype diversity—especially in Spain (ES)—suggests potential associations with intensive production systems. Overall, this large European survey indicates frequent circulation of swIAV within the targeted study population, accompanied by high genetic diversity and ongoing reassortment, underscoring the need for harmonized genomic surveillance to inform veterinary and public health preparedness.

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Cite

BibTeXRIS
BibTeX
@article{lilliejaschniski2026largescale,
  title = {{Large‐Scale Genomic Surveillance of Swine Influenza A Viruses in Europe Highlights Increased Reassortment Potential and Field‐Based Associations With Clinical Manifestations}},
  author = {Kathrin Lillie-Jaschniski and Zalán Homonnay and Gwenaëlle Dauphin and István Kiss and Susanne Zoels and Julia Stadler and Nick Vereecke},
  journal = {Transboundary and Emerging Diseases},
  year = {2026},
  month = nov,
  doi = {10.1155/tbed/7198173},
  url = {https://doi.org/10.1155/tbed/7198173},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Large‐Scale Genomic Surveillance of Swine Influenza A Viruses in Europe Highlights Increased Reassortment Potential and Field‐Based Associations With Clinical Manifestations
AU  - Kathrin Lillie-Jaschniski
AU  - Zalán Homonnay
AU  - Gwenaëlle Dauphin
AU  - István Kiss
AU  - Susanne Zoels
AU  - Julia Stadler
AU  - Nick Vereecke
PY  - 2026
DA  - 2026/11/01
JO  - Transboundary and Emerging Diseases
DO  - 10.1155/tbed/7198173
UR  - https://doi.org/10.1155/tbed/7198173
AB  - Swine influenza A virus (swIAV) is an important One Health pathogen due to its genetic diversity, ongoing reassortment, and implications for animal and public health. Between 2022 and 2023, nasal swabs (NSs) from pigs of multiple age groups were collected from 134 farms across 16 European countries and analyzed by real‐time quantitative PCR (RT‐qPCR), subtyping, and whole‐genome sequencing. Clinical and management metadata were integrated with viral genotypes. swIAV was detected in 93% of the targeted farms included in this study, with Clade 1A (H1pdmN1) and Clade 1C (H1avN1, H1avN2, and H1huN2) predominating. Sequencing identified 23 genotypes, including 12 previously unreported ones. Exploratory analysis suggested potential associations between specific hemagglutinin (HA) (sub)clades and clinical signs in piglets and with herd management factors. High genotype diversity—especially in Spain (ES)—suggests potential associations with intensive production systems. Overall, this large European survey indicates frequent circulation of swIAV within the targeted study population, accompanied by high genetic diversity and ongoing reassortment, underscoring the need for harmonized genomic surveillance to inform veterinary and public health preparedness.
SN  - 1865-1674
SN  - 1865-1682
ER  -