Continual Reintroduction of Human Pandemic H1N1 Influenza A

The diversity of influenzaA viruses in swine (swIAVs) presents an important pandemic threat. Knowledge of the human-swine inter-face is particularly important for understanding howviruseswith pandemic potential evolve in swine hosts. Throughphylogenetic analysis of contemporary swIAVs in theUnited States, we demonstrate that human-to-swine transmission of pandemicH1N1 (pH1N1) viruses has occurred continuously in the years following the 2009H1N1pandemic andhas been an important contributor to the genetic diversity ofU.S. swIAVs. AlthoughpandemicH1 andN1 segments had been largely removed from theU.S. swine popula-tion by 2013 via reassortmentwith other swIAVs, these antigens reemerged followingmultiple human-to-swine transmission events during the 2013-2014 seasonal epidemic. These findings indicate that the six internal gene segments frompH1N1 viruses are likely to be sustained long term in theU.S. swine population,with periodic reemergence of pandemic hemagglutinin (HA) andneuraminidase (NA) segments in associationwith seasonal pH1N1 epidemics in humans. VaccinatingU.S. swineworkersmay reduce infection of both humans and swine and in turn limit the role of humans as sources of influenza virus diversity in pigs. IMPORTANCE Swine are important hosts in the evolution of influenzaA viruseswith pandemic potential. Here, we analyze influenza virus sequence data generated by theU.S.Department of Agriculture’s national surveillance system to identify the central role of humans in the re-emergence of pandemicH1N1 (pH1N1) influenza viruses inU.S. swine herds in 2014. These findings emphasize the important role o