Substitutions near the Hemagglutinin Receptor-Binding Site Determine the Antigenic Evolution of Influenza A H3N2 Viruses in U.S. Swine

Abstract

Swine influenza A virus is an endemic and economically important pathogen in pigs, with the potential to infect other host species. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major component in swine influenza A vaccines. However, as a result of antigenic drift, vaccine strains must be regularly updated to reflect currently circulating strains. Characterizing the cross-reactivity between strains in pigs and seasonal influenza virus strains in humans is also important in assessing the relative risk of interspecies transmission of viruses from one host population to the other. Hemagglutination inhibition (HI) assay data for swine and human H3N2 viruses were used with antigenic cartography to quantify the antigenic differences among H3N2 viruses isolated from pigs in the United States from 1998 to 2013 and the relative cross-reactivity between these viruses and current human seasonal influenza A virus strains. Two primary antigenic clusters were found circulating in the pig population, but with enough diversity within and between the clusters to suggest updates in vaccine strains are needed. We identified single amino acid substitutions that are likely responsible for antigenic differences between the two primary antigenic clusters and between each antigenic cluster and outliers. The antigenic distance between current seasonal influenza virus H3 strains in humans and those endemic in swine suggests that population immunity may not prevent the introduction of human viruses into pigs, and possibly vice versa, reinforcing the need to monitor and prepare for potential incursions. IMPORTANCEInfluenza A virus (IAV) is an important pathogen in pigs and humans. The hemagglutinin (HA) protein is the primary target of protective immune responses and the major target of vaccines. However, vaccine strains must be updated to reflect current strains. Characterizing the differences between seasonal IAV in humans and swine IAV is important in assessing the relative risk of interspecies transmission of viruses. We found two primary antigenic clusters of H3N2 in the U.S. pig population, with enough diversity to suggest updates in swine vaccine strains are needed. We identified changes in the HA protein that are likely responsible for these differences and that may be useful in predicting when vaccines need to be updated. The difference between human H3N2 viruses and those in swine is enough that population immunity is unlikely to prevent new introductions of human IAV into pigs or vice versa, reinforcing the need to monitor and prepare for potential introductions.

Amino Acids in Hemagglutinin Antigenic Site B Determine Antigenic and Receptor Binding Differences between A(H3N2)v and Ancestral Seasonal H3N2 Influenza Viruses

“…The amino acid residues identified in the present study as critical for the antigenic difference between A(H3N2)v and seasonal H3N2 viruses are all located near the RBS in HA, which is in agreement with the observations in other studies that examined H3N2 antigenic evolution (19,23,24). Our study indicated that the amino acid mutations which switched the antigenic phenotype of MN/10 and BJ/92 influenced receptor binding.…”

“…A(H3N2)v isolates are antigenically distinct from recent human seasonal H3N2 viruses as well as H3N2 viruses that circulated in humans during the period when they are thought to have been introduced into swine (2,3,19). Although amino acids close to the receptor binding site (RBS) in hemagglutinin (HA) are associated with antigenic evolution of human seasonal H3N2 and swine H3N2 viruses (23,24), the specific residues that explain why swine-origin A(H3N2)v viruses are antigenically distinct from the human strains have not been identified.…”

“…Outbreaks of TRIG-H3N2 virus infections in U.S. swine were first reported in a few states in 1998 and have spread to many other states (11) and Canada (17,18). The current circulating swine H3N2 viruses in North America, together with A(H3N2)v viruses, were termed "lineage IV" based on the phylogenetic analysis with earlier swine H3N2 isolates (13,(17)(18)(19). The majority of A(H3N2)v isolates since 2011 have acquired the matrix gene from the 2009 pandemic H1N1 virus (2,20), which has enhanced the replication and transmission of A(H3N2)v viruses in swine (21,22), potentially increasing the risk of human infection.…”

Novel Reassortant Human-Like H3N2 and H3N1 Influenza A Viruses Detected in Pigs Are Virulent and Antigenically Distinct from Swine Viruses Endemic to the United States

“…Two-way HI assays against a reference swine antiserum panel (see Table S3 in the supplemental material) were performed as described above, using a panel of reference swine and human H3N2 viruses, including Sw/MO/12, Sw/MO/14, and A/VIC/11, as HI antigens (28). The reference panel represents H3 viruses historically or currently circulating in pigs in the United States, along with recent and historical representatives of human vaccine strains.…”

New reassortant and enzootic European swine influenza viruses transmit efficiently through direct contact in the ferret model

“…A recent study did show that contemporary human seasonal H3N2 viruses had obtained substantial antigenic distance from swine H3N2 viruses, even though the lineages shared a common ancestor. Hence, the authors speculated that this increasing distance could pose a risk for the youngest of the human population, as they could become increasingly susceptible to infections with swine H3N2 due to the lack of cross-reacting immunity (Lewis et al, 2014). These findings stress the need for a continued and systematic surveillance of European swine influenza viruses in order to detect new reassortants, as well as monitoring the evolution and zoonotic potential of both reassortant and enzootic swine influenza virus strains.…”