1. Microbiology and Infectious Disease
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Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses

  1. Pia Ryt-Hansen  Is a corresponding author
  2. Jesper Schak Krog
  3. Solvej Østergaard Breum
  4. Charlotte Kristiane Hjulsager
  5. Anders Gorm Pedersen
  6. Ramona Trebbien
  7. Lars Erik Larsen
  1. University of Copenhagen, Denmark
  2. Statens Serum Institut, Denmark
  3. Technical University of Denmark, Denmark
Research Article
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Cite this article as: eLife 2021;10:e60940 doi: 10.7554/eLife.60940

Abstract

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV positive submissions, reaching 56% in 2018. Full genome sequences were obtained from 129 swIAV positive samples. Altogether, 17 different circulating genotypes were identified including six novel reassortants harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx (clade 1A.3.3.2) viruses. The results provide essential data for the control of swIAV in pigs and emphasize the importance of contemporary surveillance for discovering novel swIAV strains posing a potential threat to the human population.

Data availability

All sequences generated in the study have been uploaded in NCBI GenBank with accession numbers MT666225 - MT667233, and will be released upon acceptance of the manuscript. All analyses of the sequences are included in the manuscripts or in the supplement files and figures.

Article and author information

Author details

  1. Pia Ryt-Hansen

    Department of Health Sciences, Institute for Animal and Veterinary Sciences, University of Copenhagen, Frederiksberg C, Denmark
    For correspondence
    piarh@sund.ku.dk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4819-6869
  2. Jesper Schak Krog

    Virus & Mikrobiologisk Specialdiagnostik, Statens Serum Institut, Copenhagen S, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  3. Solvej Østergaard Breum

    Virus & Mikrobiologisk Specialdiagnostik, Statens Serum Institut, Copenhagen S, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  4. Charlotte Kristiane Hjulsager

    Virus & Mikrobiologisk Specialdiagnostik, Statens Serum Institut, Copenhagen S, Denmark
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7557-8876
  5. Anders Gorm Pedersen

    Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  6. Ramona Trebbien

    Virus & Mikrobiologisk Specialdiagnostik, Statens Serum Institut, Copenhagen S, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  7. Lars Erik Larsen

    Department of Health Sciences, Institute for Animal and Veterinary Sciences, University of Copenhagen, Frederiksberg C, Denmark
    Competing interests
    The authors declare that no competing interests exist.

Funding

Novo Nordisk Foundation (NNF19OC0056326)

  • Lars Erik Larsen

IDT Biologika GmbH (SwIAV surveillance)

  • Pia Ryt-Hansen
  • Jesper Schak Krog
  • Solvej Østergaard Breum
  • Charlotte Kristiane Hjulsager
  • Anders Gorm Pedersen
  • Ramona Trebbien
  • Lars Erik Larsen

Danish Veterinary and Food Administration (SwIAV surveillance)

  • Pia Ryt-Hansen
  • Jesper Schak Krog
  • Solvej Østergaard Breum
  • Charlotte Kristiane Hjulsager
  • Anders Gorm Pedersen
  • Ramona Trebbien
  • Lars Erik Larsen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Jos W Van der Meer, Radboud University Medical Centre, Netherlands

Publication history

  1. Received: July 10, 2020
  2. Preprint posted: July 29, 2020 (view preprint)
  3. Accepted: July 21, 2021
  4. Accepted Manuscript published: July 27, 2021 (version 1)
  5. Version of Record published: August 27, 2021 (version 2)

Copyright

© 2021, Ryt-Hansen et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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