Diverse Genomic Landscape of Swine Influenza A Virus in England (2014 - 2021)

Abstract

Surveillance of influenza A viruses in pigs (SwIAV) is critical for identification of novel genetic groups that pose a risk to pig health and might have zoonotic potential. SwIAVs circulating in pigs in England between 2014 and 2021 were characterised using whole genome sequencing (WGS). Haemagglutinin (HA) and neuraminidase (NA) sequencing data from 82 of 368 influenza A positive samples (71 submissions) were determined, identifying H1N1 and H1N2 subtypes from the 1A classical swine and 1B human-seasonal lineages respectively. The 1B lineage viruses were predominant, accounting for 68.29% of sequenced viruses, with 1A lineage viruses comprising 31.71%, primarily from the 1A.3.3.2 clade (2009 H1N1 pandemic origin). This study characterised previously undefined diversity within the 1B lineage which led to the designation of new HA clades 1B.1.1.1, 1B.1.1.2 and 1B.1.1.3. Complete genome data were obtained from 64/82 viruses thereby updating the definition of genetic diversity thresholds and leading to the identification of 24 unique genotypes. All these 64 viruses contained PB2, PB1, PA, NP, MP, and NS gene segments of 2009 H1N1 pandemic origin. These data highlight the increasing divergence of SwIAV within pig populations England and emphasise the requirement for continued genomic surveillance to improve animal health and monitor zoonotic risk.