The role of swine as "mixing vessel" for interspecies transmission of the influenza A subtype H1N1: a simultaneous Bayesian inference of phylogeny and ancestral hosts.

Condensing the information of a total of 1551 to 469 influenza A H1N1 isolates we investigated the frequency of host shifts among bird, human and swine. Phylogenies of hemagglutinin and neuraminidase as well as ancestral host reconstructions were simultaneously inferred in a Bayesian framework. The surface proteins had to be analyzed separately because of reassortment. Also the different tree topologies indicated the different evolutionary histories of these genes. The majority of interspecies transmissions involved isolates from swine confirming the role of pigs as "mixing vessel" for the influenza A virus. This was emphasized by the investigation of host specific amino acid positions. However, the simultaneous estimation of phylogeny and ancestral states resulted in considerable ambiguity in particular at deeper nodes and at the root cautioning against overstated conclusions. Our analysis highlights the urge of intensifying influenza surveillance programs for porcine hosts.