OFFLU Swine Influenza Report: July 2021 to December 2021

Authors: MARKIN, ALEXEY - Oak Ridge Institute For Science And Education (ORISE); HUFNAGEL, DAVID - Oak Ridge Institute For Science And Education (ORISE); ARENDSEE, ZEBULUN - Oak Ridge Institute For Science And Education (ORISE); SNYDER, CELESTE - Oak Ridge Institute For Science And Education (ORISE); JANAS-MARTINDALE, ALICIA - Animal And Plant Health Inspection Service (APHIS); INDERSKI, BLAKE - Oak Ridge Institute For Science And Education (ORISE); BROWN, IAN - Animal & Plant Health Agency Apha; Anderson, Tavis; LEWIS, NICOLA - Royal Veterinary College; Baker, Amy; COGGON, AMELIA - Royal Veterinary College; SARA, LOPES - Royal Veterinary College; JAMES, JOE - Animal & Plant Health Agency Apha; MOLLET, BENJAMIN - Animal & Plant Health Agency Apha; LEWIS, TOM - Animal & Plant Health Agency Apha

Submitted to: World Health Organization
Publication Type: Government Publication
Publication Acceptance Date: 4/22/2022
Publication Date: 4/22/2022
Citation: Markin, A., Hufnagel, D.E., Arendsee, Z., Snyder, C., Janas-Martindale, A., Inderski, B., Brown, I., Anderson, T.K., Lewis, N.S., Baker, A.L., Coggon, A., Sara, L., James, J., Mollet, B., Lewis, T. 2022. OFFLU Swine Influenza Report: July 2021 to December 2021. Technical report generated for the World Health Organization (WHO) Vaccine Consultation Meeting. p.62.

Interpretive Summary:

Technical Abstract: H1N1, H1N2, and H3N2 influenza A virus (IAV) subtypes are endemic in swine herds around the world. Swine H1 genes are classified into three major genetic lineages: 1A, 1B, and 1C . The 1A lineage arose from the 1918 human pandemic H1N1, with global introductions into swine and subsequent transmission and migration. The 1B lineage resulted from repeated independent global introductions of human seasonal H1 IAVs into swine. The 1C lineage arose from an avian IAV spillover into swine. Swine H3 viruses also arose from multiple independent introductions from human seasonal H3N2. H3 genes in swine are classified by the decade of introduction, 1970s, 1990s, and 2010s. Since 2009, frequent human to swine transmission of H1N1pdm09 (clade 1A.3.3.2) IAV occurred and viral diversity in all swine IAV lineages increased after reassortment with co-circulating H1N1pdm virus internal genes. Because of the risk animal IAV pose to the human population, experts at the World Health Organization (WHO) vaccine composition meeting review zoonotic cases and consider them for development of pandemic-preparedness candidate vaccine viruses (CVV). Few of the genetic clades globally detected in swine currently contain a CVV and those available may not provide protection given observed genetic and antigenic differences in circulating swine viruses. Human and swine IAV evolution are entwined, particularly since 2009, therefore, a system to prioritize and evaluate evolving swine IAV in the context of human risk should be part of a comprehensive pandemic preparedness plan. We quantified the global genetic diversity of swine IAV circulating from July 2021 to December 2021; and determined how similar the circulating swine IAV was to human IAV vaccines and current candidate vaccine viruses (CVV) that are used for pandemic preparedness. We also antigenically characterized a subset of viruses representing circulating swine IAV using a panel of monovalent anti-sera raised in ferrets against human vaccine strains or CVV strains in hemagglutination inhibition (HI) assays. The data demonstrated 19 genetically distinct cocirculating swine IAV clades. 21 human variant cases with IAV of swine origin were identified, with variants distributed across nine of the 19 swine HA genetic clades. The phylogenetically characterized swine HA genes were significantly different to the current H1 and H3 components of human IAV vaccines. Antigenic characterization demonstrated that 15 of the 19 distinct swine genetic clades had significantly reduced cross-reactivity to CVV or vaccine strain antisera, identifying gaps of coverage by human pandemic preparedness vaccines. 7 of the 15 have a history of a known human zoonotic variant case. These analyses demonstrate the dynamic interplay of IAV transmission between humans and swine, and identify genetic groups that should be considered within a systematic analysis of swine IAV as a risk to the human population.