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. 2023 Sep 7;15(9):1893.
doi: 10.3390/v15091893.

Genetic Diversity of Type A Influenza Viruses Found in Swine Herds in Northwestern Poland from 2017 to 2019: The One Health Perspective

Lukasz Rabalski  1   2 , Maciej Kosinski  1 , Piotr Cybulski  3 , Tomasz Stadejek  4 , Krzysztof Lepek  1
Affiliations

Genetic Diversity of Type A Influenza Viruses Found in Swine Herds in Northwestern Poland from 2017 to 2019: The One Health Perspective

Lukasz Rabalski et al. Viruses. .

Abstract

Influenza A viruses (IAV) are still a cause of concern for public health and veterinary services worldwide. With (-) RNA-segmented genome architecture, influenza viruses are prone to reassortment and can generate a great variety of strains, some capable of crossing interspecies barriers. Seasonal IAV strains continuously spread from humans to pigs, leading to multiple reassortation events with strains endemic to swine. Due to its high adaptability to humans, a reassortant strain based on "human-like" genes could potentially be a carrier of avian origin segments responsible for high virulence, and hence become the next pandemic strain with unseen pathogenicity. The rapid evolution of sequencing methods has provided a fast and cost-efficient way to assess the genetic diversity of IAV. In this study, we investigated the genetic diversity of swine influenza viruses (swIAVs) collected from Polish farms. A total of 376 samples were collected from 11 farms. The infection was confirmed in 112 cases. The isolates were subjected to next-generation sequencing (NGS), resulting in 93 full genome sequences. Phylogenetic analysis classified 59 isolates as genotype T (H1avN2g) and 34 isolates as genotype P (H1pdmN1pdm), all of which had an internal gene cassette (IGC) derived from the H1N1pdm09-like strain. These data are consistent with evolutionary trends in European swIAVs. The applied methodology proved to be useful in monitoring the genetic diversity of IAV at the human-animal interface.

Keywords: NGS sequencing; emerging diseases; epidemiology; influenza; surveillance; zoonosis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Maximum Likelihood (ML) phylogeny tree of segment HA of swine influenza viruses analyzed in this work. The tree was inferred using relevant swIAV strains representing major European lineages, human reference strains associated with “human-like” swIAVs, and recent Polish isolates. The reference dataset was retrieved from the GenBank Influenza Virus Resource Database and the GISAID EpiFlu™ database. The Polish isolate names from this study are marked in red, and recent Polish isolates are marked in blue. Known reference strains and those circulating in Europe are denoted in black. The major lineages are highlighted in color: H1 avian-like swine (Eurasian Avian), blue; H1 Pdm09 (Classical swine), green; H1 human-like swine (Human seasonal), orange; H3 human-like swine, beige. The tree was drawn to scale and validated by 1000 bootstrap replicates, with branch lengths indicative of the number of substitutions per site.
Figure 2
Figure 2
Maximum Likelihood (ML) phylogeny tree of segment NA of swine influenza viruses analyzed in this work. The tree was inferred using relevant swIAV strains representing major European lineages, human reference strains associated with “human-like” swIAVs, and recent Polish isolates. The reference dataset was retrieved from the GenBank Influenza Virus Resource Database and the GISAID EpiFlu™ database. The Polish isolate names from this study are marked in red, and recent Polish isolates are marked in blue. Known reference strains and those circulating in Europe are denoted in black. The major lineages are highlighted in color: N2g (A/swine/Gent/1/1984-like), orange; N2s (A/swine/Scotland/410440/94-like), gray; Seasonal H3N2, pink; It-N2 (A/swine/Italy/4675/2003-like), red; N1 Pdm09, green; N1 avian-like swine, blue. The tree was drawn to scale and validated by 1000 bootstrap replicates, with branch lengths indicative of the number of substitutions per site.
Figure 3
Figure 3
Maximum Likelihood (ML) phylogeny tree of segment PB2 of swine influenza viruses analyzed in this work. The tree was inferred using relevant swIAV strains representing major European lineages, human reference strains associated with “human-like” swIAVs, and recent Polish isolates. The reference dataset was retrieved from the GenBank Influenza Virus Resource Database and the GISAID EpiFlu™ database. The Polish isolate names from this study are marked in red, and recent Polish isolates are marked in blue. Known reference strains and those circulating in Europe are denoted in black. The major lineages are highlighted in color: PB2 Pdm09, green; Pb2 avian-like, blue. The tree was drawn to scale and validated by 1000 bootstrap replicates, with branch lengths indicative of the number of substitutions per site.
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