Evolution and antigenic advancement of N2 neuraminidase of swine influenza A viruses circulating in the United States following two separate introductions from human seasonal viruses

Authors: KAPLAN, BRYAN - Orise Fellow; Anderson, Tavis; CHANG, JENNIFER - Orise Fellow; SANTOS, JEFFERSON - University Of Georgia; PEREZ, DANIEL - University Of Georgia; LEWIS, NICOLA - Royal Veterinary College; Baker, Amy

Submitted to: Journal of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/15/2021
Publication Date: 9/27/2021
Citation: Kaplan, B.S., Anderson, T.K., Chang, J., Santos, J., Perez, D., Lewis, N., Vincent, A.L. 2021. Evolution and antigenic advancement of N2 neuraminidase of swine influenza A viruses circulating in the United States following two separate introductions from human seasonal viruses. Journal of Virology. 95(20). https://journals.asm.org/doi/10.1128/JVI.00632-21.
DOI: https://doi.org/10.1128/JVI.00632-21

Interpretive Summary: The influenza A virus (IAV) neuraminidase (NA) gene of the N2 subtype currently accounts for approximately two-thirds of the NA detections in US domestic swine populations. These N2 genes have undergone substantial genetic and antigenic evolution following two separate introductions of human seasonal N2 into swine in 1998 and 2002. Increased genetic diversity of the N2 gene suggested an increase in antigenic evolution of the virus surface glycoprotein, and may allow escape from natural and/or vaccine induced immunity. To assess the potential loss in immune recognition among naturally occurring N2 from swine, we characterized the antigenic evolution of swine IAV by generating a panel of antisera against representative N2 and quantified the antigenic distance between wild-type viruses using an enzyme-linked lectin assay and antigenic cartography. We found in the 20+ years following the introduction, the genetic diversity of N2 in swine increased. This corresponded with an increase in antigenic diversity. Antibodies generated against representative N2 of the 1998 N2 did not inhibit N2 activity of the 2002 lineage and vice versa. Further, both the 1998 and 2002 N2 lineages displayed antigenic drift, indicating the N2 in US swine harbors a substantial amount of antigenic diversity. Continued research into the antigenic diversity of N2 in swine will aid vaccine design and prevention strategies.

Technical Abstract: Two separate introductions of human seasonal N2 neuraminidase genes were sustained in United States swine since 1998 (N2-98) and 2002 (N2-02). Herein, we characterized the antigenic evolution of the N2 of swine influenza A virus (IAV) across two decades following the two introductions. The N2-98 and N2-02 expanded in genetic diversity, with two statistically supported monophyletic clades within each lineage. To assess antigenic drift in swine N2 following the human-to-swine spillover events, we generated a panel of swine N2 antisera against representative N2 and quantified the antigenic distance between wild-type viruses using enzyme-linked lectin assay and antigenic cartography. The antigenic distance between swine and human N2 was smallest between human N2 circulating at the time of each introduction and the archetypal swine N2. However, sustained circulation and evolution in swine of the two N2 lineages resulted in significant antigenic drift, and the N2-98 and N2-02 swine N2 lineages were antigenically distinct. Although there was within-lineage antigenic diversity, the differences between viruses within each identified genetic clade was not always indicative of significant antigenic drift. These data represent the first quantification of the antigenic diversity of neuraminidase of IAV in swine and demonstrated significant antigenic drift from contemporary human seasonal strains as well as antigenic variation among N2 detected in swine. These data suggest that antigenic mismatch may occur between circulating swine IAV and vaccine strains. Consequently, consideration of the diversity of N2 in swine IAV vaccines will likely result in more effective control, and aid public health initiatives where candidate vaccine viruses are selected for pandemic preparedness. Antibodies inhibiting the neuraminidase (NA) of influenza A virus (IAV) reduce clinical disease and virus shedding and contribute to reduced IAV transmission in the absence of neutralizing immunity against the hemagglutinin. To understand antibody recognition of the genetically diverse NA in U.S. swine IAV, we characterized the antigenic diversity of N2 from swine and humans. N2 detected in swine IAV across the last twenty years were derived from two distinct human-to-swine spillovers that have persisted, are antigenically distinct, and have undergone antigenic drift. These findings highlight the need for continued surveillance and vaccine development in swine with increased focus on the NA. Additionally, human seasonal N2 isolated after 2005 were poorly inhibited by representative swine N2 antisera, suggesting a lack of cross-reactive NA antibody mediated immunity between contemporary swine and human N2. Bidirectional transmission between humans and swine represents a One Health challenge, and determining the correlates of immunity to emerging IAV strains is critical to mitigate zoonotic and reverse-zoonotic transmission.