ARS | Publication request: Increased diversity of H3N2 influenza virus in pigs in the United States and implications for pigs and humans

Submitted to: American Society for Virology Meeting
Publication Type: Abstract Only
Publication Acceptance Date: March 12, 2013
Publication Date: N/A

Technical Abstract: In 2011-2012 at least 320 human cases of H3N2 (H3N2v) viruses closely related to swine influenza A viruses (IAV) were detected in the United States. We performed phylogenetic analysis of 200 whole genome sequences of North American swine IAV to identify reassortment events and compare these novel gene constellation patterns in swine IAV with H3N2v. Viruses included 119 swine H3N2, 67 swine H1N1, and 14 human H3N2v viruses collected during 2009-2012. All H3 hemagglutinin (HA) genes evolved from the prototypical North American H3 cluster 4, with evidence for further diversification into potential sub-clusters. At least 10 distinct reassorted H3N2/H1N1pdm09 (rH3N2p) genotypes (G1-G10) based on lineage of each gene segment were identified in swine. Genotype 1 acquired the M gene alone from H1N1pdm09 similar to H3N2v, and was most frequently detected among rH3N2p in pigs, indicating a possible genetic fitness of this gene combination in swine and potential for spillover to humans. Swine G1 viruses were positioned in two phylogenetic clades on the HA tree, representing independent evolution in swine. However, all human H3N2v included in the study clustered within a single G1 clade on all eight gene segment trees, suggesting the genetic requirements of the rH3N2p for spillover to humans is stringent. Mutations at putative antigenic sites of the HA protein of swine H3N2 viruses were detected with reduced serologic cross-reactivity among the H3 sub-clusters, demonstrating antigenic drift of these contemporary viruses. This study emphasizes the necessity for continued full genome sequencing to better understand the genetic evolution and ecology of IAV in swine and assess the role reassortment may play in antigenic evolution of the H3 in the future. Additionally, swine vaccine manufacturers should closely monitor these contemporary H3N2 for establishment of antigenic drift variants for vaccine strain purposes to protect pigs and humans.