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Research Project: Intervention Strategies to Control Influenza A Virus Infection in Swine

Location: Virus and Prion Research

Title: Increased H3 Cluster IV-A influenza A virus detection in US swine is associated with reassortment and antigenic drift

item NEVEAU, MEGAN - Iowa State University
item ZELLER, MICHAEL - Iowa State University
item GAUGER, PHILLIP - Iowa State University
item Baker, Amy
item Anderson, Tavis

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/28/2020
Publication Date: 1/11/2021
Citation: Neveau, M.N., Zeller, M.A., Gauger, P.C., Vincent, A.L., Anderson, T.K. 2021. Increased H3 Cluster IV-A influenza A virus detection in US swine is associated with reassortment and antigenic drift [abstract]. Centers of Excellence for Influenza Research and Surveillance Annual Network Meeting. Poster No. 114.

Interpretive Summary:

Technical Abstract: H3 cluster IV-A (CIV-A; H3.1990.4) influenza A viruses (IAV) in swine originated from a 1990s human seasonal transmission event and composed the majority of H3 US swine detections for two decades. This lineage was surpassed in relative frequency from 2016 to 2020 by a more recent human-to-swine lineage (H3.2010.1). However, passive surveillance indicated an increase in the detections of the H3.1990.4 hemagglutinin (HA) genes in US swine beginning in April 2019. We conducted phylogenetic analyses to investigate potential factors associated with the increase. A phylodynamic analysis of the HA gene documented low relative genetic diversity within the contemporary clades, suggesting clonal expansion of genetically similar viruses. We adapted Nextstrain for swine IAV and identified HA amino acid mutations. These data showed two concurrent circulating clades across multiple US states. The clade with the majority of recent detections had an amino acid substitution at position 156, a site previously determined to affect antigenic phenotype, changing the predominant antigenic motif from NYNNYK to NYHNYK. Whole genome sequences from 19 isolates were used to assess whether whole genome constellation and reassortment were associated with increased detection frequency. Reassortment was observed in both cocirculating clades: the minor clade was paired with N2-2002B in ancestral strains, but more recently with N2-2002A; in the major clade, nucleoprotein (NP) from the TRIG lineage was replaced with NP of the pandemic lineage. We then selected strains with representative HA genes from each of increasing H3 CIV-A clades to assess the antigenic phenotype using hemagglutination inhibition (HI) assays. Defining the genetic and antigenic factors contributing to the expansion of these CIV-A clades is essential to understanding and predicting mechanisms that viruses employ to evade current control measures.