Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses
- University of Copenhagen, Denmark
- Statens Serum Institut, Denmark
- Technical University of Denmark, Denmark
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
Charlotte Kristiane Hjulsager
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.
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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Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses
eLife 10:e60940.
https://doi.org/10.7554/eLife.60940
