Diverse genomic landscape of swine influenza A virus in England (2014–2021)

Authors: MOLLETT, BENJAMIN - Animal & Plant Health Agency Apha; BYRNE, ALEXANDER - Royal Veterinary College; EVERETT, HELEN - Animal & Plant Health Agency Apha; REID, SCOTT - Animal & Plant Health Agency Apha; WILLIAMSON, SUSANNA - Animal & Plant Health Agency Apha; Anderson, Tavis; JAMES, JOE - Animal & Plant Health Agency Apha; BANYARD, ASHLEY - Animal & Plant Health Agency Apha; BROWN, IAN - The Pirbright Institute; LEWIS, NICOLA - Royal Veterinary College

Submitted to: Microbial Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/26/2026
Publication Date: 3/19/2026
Citation: Mollett, B.C., Byrne, A.M., Everett, H.E., Reid, S.M., Williamson, S., Anderson, T.K., James, J., Banyard, A.C., Brown, I.H., Lewis, N.S. 2026. Diverse genomic landscape of swine influenza A virus in England (2014–2021). Microbial Genomics. https://doi.org/10.1099/mgen.0.001668.
DOI: https://doi.org/10.1099/mgen.0.001668

Interpretive Summary: Variation in the genetic diversity of influenza A virus (IAV) in swine through time and between regions impacts control efforts. This study quantified the genomic diversity of swine IAV collected from 2012 to 2021 in England at regional and national levels. These data provide a baseline measure of genetic diversity that can be used to identify vaccine targets and detect novel viruses that impact animal and public health. We quantified the co-circulation of 1A classical swine lineage viruses and pre-2009 1B human seasonal influenza viruses: the viruses in pigs in England were distinct from other groups of viruses detected in global swine populations. The diversity within the 1B viruses in pigs was significant, and there were three groupings that warranted new names to facilitate communication with producers, veterinarians, and public health agencies. When analyzing the genomes of the viruses collected in pigs, there were 24 different combinations of genes. and all of the viruses had components derived from the 2009 H1N1 swine-origin pandemic. We show how passive surveillance can be used to design vaccine interventions that target swine IAV diversity to reduce or minimize the emergence of genomic diversity, and demonstrate how these efforts are likely to reduce the transmission of swine IAV within pigs and between swine and humans.

Technical Abstract: Surveillance of swine influenza A viruses (SwIAV) in pigs is critical for identification of novel genetic groups that pose a risk to pig health and might have greater zoonotic potential. SwIAVs circulating in pigs in Great Britain between 2014 and 2021 were characterised using whole genome sequencing (WGS). Hemagglutinin (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 lineage, 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 of the subtyped viruses allowing for the definition of genetic diversity thresholds leading to the identification of 24 unique genotypes. All 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 in Great Britain and emphasise the requirement for continued genomic surveillance to improve animal health.