Introductions and evolution of human-origin seasonal influenza a viruses in multinational swine populations

Abstract

The capacity of influenza A viruses to cross species barriers presents a continual threat to human and animal health. Knowledge of the human-swine interface is particularly important for understanding how viruses with pandemic potential evolve in swine hosts. We sequenced the genomes of 141 influenza viruses collected from North American swine during 2002 to 2011 and identified a swine virus that possessed all eight genome segments of human seasonal A/H3N2 virus origin. A molecular clock analysis indicates that this virus--A/sw/Saskatchewan/02903/2009(H3N2)--has likely circulated undetected in swine for at least 7 years. For historical context, we performed a comprehensive phylogenetic analysis of an additional 1,404 whole-genome sequences from swine influenza A viruses collected globally during 1931 to 2013. Human-to-swine transmission occurred frequently over this time period, with 20 discrete introductions of human seasonal influenza A viruses showing sustained onward transmission in swine for at least 1 year since 1965. Notably, human-origin hemagglutinin (H1 and H3) and neuraminidase (particularly N2) segments were detected in swine at a much higher rate than the six internal gene segments, suggesting an association between the acquisition of swine-origin internal genes via reassortment and the adaptation of human influenza viruses to new swine hosts. Further understanding of the fitness constraints on the adaptation of human viruses to swine, and vice versa, at a genomic level is central to understanding the complex multihost ecology of influenza and the disease threats that swine and humans pose to each other.

Importance: The swine origin of the 2009 A/H1N1 pandemic virus underscored the importance of understanding how influenza A virus evolves in these animals hosts. While the importance of reassortment in generating genetically diverse influenza viruses in swine is well documented, the role of human-to-swine transmission has not been as intensively studied. Through a large-scale sequencing effort, we identified a novel influenza virus of wholly human origin that has been circulating undetected in swine for at least 7 years. In addition, we demonstrate that human-to-swine transmission has occurred frequently on a global scale over the past decades but that there is little persistence of human virus internal gene segments in swine.

FIG 1

Phylogenetic relationships between human and swine H3 segments. A time-scaled Bayesian MCC tree inferred for the HA (H3) sequences of 208 swine IAVs identified as of human seasonal virus origin and 251 human seasonal H3N2 influenza viruses, collected 1968 to 2013, is shown. Branches of human seasonal H3N2 influenza virus origin are in black, while branches associated with viruses from swine are shaded by country or continent of origin: ARG, Argentina; CAN, Canada; CHN, China (including Hong Kong SAR and Taiwan); EUR, Europe; KOR, South Korea; MEX, Mexico; THA, Thailand; VNM, Vietnam. Posterior probabilities of >0.9 are included for key nodes, and the 10 discrete introductions of the human H3 segment into swine that are supported by high posterior probabilities and long branch lengths are labeled according to Table 1.

FIG 2

Introductions of human seasonal influenza viruses into swine, 1965 to 2013. A summary of the 20 introductions of seasonal human IAVs into swine resulting in sustained transmission in swine (for at least 1 year) by segment and region. Introductions involving the HA and NA segments are depicted in the upper portion of the figure, and the subset involving internal gene segments are presented in the lower portion. Each colored line represents a human-to-swine transmission event of a segment. Introductions are numbered 1 to 20 in accordance with Table 1. The timing of each human-to-swine transmission event is estimated from the tMRCAs inferred from the MCC trees, with gray boxes indicating the 95% HPD interval between the swine clade and most closely related human viruses and the black box indicating the 95% HPD interval for the swine clade only. Each line extends forward in time up to the most recently sampled swine virus of that lineage.

FIG 3

Phylogenetic relationships between human and swine N2 segments. A time-scaled Bayesian MCC tree inferred for the NA (N2) sequences of 350 swine influenza viruses identified as of human seasonal virus origin and 325 human H3N2 and H1N2 seasonal influenza viruses, collected from 1957 to 2013, is shown. Labeling and shading are similar to those in Fig. 1.

FIG 4

Phylogenetic relationships between seasonal human and swine H1 segments. A time-scaled Bayesian MCC tree inferred for HA (H1) sequences of 84 swine influenza viruses identified as of human seasonal virus origin and 108 human seasonal H1N1 and H1N2 influenza viruses, collected from 1977 to 2009, is shown. Labeling and shading are similar to those in Fig. 1.