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

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.

Genomic diversity and evolutionary dynamics of Influenza A viruses in Colombian swine: implications for one health surveillance and control

“…The swine IAV from this study revealed a wide genotypic diversity in the study period, with most of the viruses belonging to 2009 pandemic lineage (H1N1pdm09). This is consistent with other reports in swine in the region and globally [ 7 , 19 , 29 ]. The genetic makeup of the pandemic H1 genes analysed in this study and their close relationship with pandemic and seasonal human IAV may suggest that these viruses continuously circulate within the swine population, possibly as a result of multiple reverse zoonotic events as reported in other studies [ 47–49 ].…”

“…Swine influenza viruses (SIV) are genetically diverse and classified into various genotypes based on their genetic makeup. These genotypes result from frequent reassortment events between swine, avian, and human influenza viruses [ 7 ]. The primary SIV genotypes include H1N1, H3N2, and H1N2, each with multiple lineages and sub-lineages reflecting their complex evolutionary history.…”