Genetic and antigenic evolution of H1 swine influenza A viruses isolated in Belgium and the Netherlands from 2014 through 2019

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.

Mapping SARS-CoV-2 antigenic relationships and serological responses

“…However, as the number of variants continues to increase, the task of understanding the antigenic relationships among variants from raw neutralization titer data becomes increasingly complex. Antigenic cartography ( 14) is a tool originally developed for the analysis of human seasonal influenza virus antigenic data and has since been used in the analysis of antigenic variation in other pathogens, including avian, equine and swine influenza viruses (15)(16)(17)(18)(19), flaviviruses (20) including dengue viruses (21,22), lyssaviruses (23), and foot-and-mouth disease viruses (24). It allows a quantitative and visual summary of antigenic differences among a large number of variants and is a core component of the bi-annual influenza virus vaccine strain selection process convened by the WHO.…”

Genetic Variability among Swine Influenza Viruses in Italy: Data Analysis of the Period 2017–2020

“…Viruses 2022, 14, 47 2 of 17 Recently, a new H1 nomenclature was proposed to better classify universally H1 lineages: the HA-1A classical lineage, which also includes the H1N1pdm09 lineage, related to the 1918 human influenza pandemic; HA-1B human seasonal lineage; and the HA-1C Eurasian avian lineage [8]. These three major lineages were further divided into second-, third-, and fourth-order clades.…”

“…Lineages of H1N1pdm09 strains adapted to swine have been described in several countries [13][14][15]. Moreover, in northern European countries (Germany, Denmark, Sweden), the H1huN2 was replaced by novel reassortant H1pdm09N2 and H1avN2 strains [14], increasing the genetic and antigenic variability described among the HA-1A and HA-1C lineages, cocirculating with different NA genes [5,6,9,[16][17][18]. The emergence of these drifted and swine-adapted strains is evidence of the active circulation of swine influenza viruses among European pig herds.…”

Improving Current Knowledge on Seroprevalence and Genetic Characterization of Swine Influenza Virus in Croatian Pig Farms: A Retrospective Study

“…Euroasian avian-like swine H1N1 viruses are the predominant viruses in the pig population in Europe, but an increasing number of reassortments between the predominant enzootic swIAVs and the H1N1pdm have been observed [33][34][35][36][37]. The enzootic H1avN1av lineage is present in most European countries and usually circulates together with reassortant strains.…”