Abstract
Surveillance of swine influenza A viruses (swIAV) allows timely detection and identification of new variants with potential zoonotic risks. In this study, we aimed to identify swIAV subtypes that circulated in pigs in Belgium and the Netherlands between 2014 and 2019, and characterize their genetic and antigenic evolution. We subtyped all isolates and analyzed hemagglutinin sequences and hemagglutination inhibition assay data for H1 swIAV, which were the dominant HA subtype. We also analyzed whole genome sequences (WGS) of selected isolates. Out of 200 samples, 89 tested positive for swIAV. swIAV of H1N1, H1N2 and H3N2 subtypes were detected. Analysis of WGS of 18 H1 swIAV isolates revealed three newly emerged genotypes. The European avian-like H1 swIAV (lineage 1C) were predominant and accounted for 47.2% of the total isolates. They were shown to evolve faster than the European human-like H1 (1B lineage) swIAV, which represented 27% of the isolates. The 2009 pandemic H1 swIAV (lineage 1A) accounted for only 5.6% of the isolates and showed divergence from their precursor virus. These results point to the increasing divergence of swIAV and stress the need for continuous surveillance of swIAV.
Highlights
Influenza A viruses of the H1N1, H1N2 and H3N2 subtypes circulate in pigs
The situation is more complex in Asia, with lineages of swine influenza A viruses (swIAV) circulating in Europe and North America circulating in this c ontinent[16,17]
Seventeen of these viruses were isolated from pigs in the Netherlands while the other 72 originated from pigs in Belgium
Summary
Influenza A viruses of the H1N1, H1N2 and H3N2 subtypes circulate in pigs. Due to the geographical segregation of pig populations and multiple introductions of viruses from either humans or birds, swine influenza A viruses (swIAV) differ genetically and antigenically between continents and regions. H1N2 viruses were first reported in 1994 and were reassortants with the HA gene of a human seasonal H1N1 virus that was circulating in the mid-1980s and all other genes from the human-like swine H3N2 virus They are referred to as the ‘human-like’ H1N2 viruses[8] and their HA belongs to lineage 1B4. The four European lineages of swIAV have continued to evolve, either through further reassortment events or accumulation of mutations in their surface protein genes, resulting in the emergence of multiple genotypes and clades of influenza viruses. This prompted the formation of the “European Surveillance Networks for Influenza in Pigs” (ESNIP 1, 2 and 3) between 2001 and 2 01318–21. The introduction of the 2009 H1N1 pandemic virus into the swine population has resulted in increased reassortment, leading to an explosion of novel genotypes of s wIAV13,23–25
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