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.

Possible sources and spreading routes of highly pathogenic avian influenza virus subtype H5N1 infections in poultry and wild birds in Central Europe in 2007 inferred through likelihood analyses.

Recurrent outbreaks of H5N1 HPAIV occurred in several Central European countries in 2007. In-depth phylogenetic analyses which included full-length genomic sequences of the viruses involved were performed to elucidate possible origins of incursions and transmission pathways. Tree reconstructions as well as host-shift and ancestral area inferences were conducted in a maximum likelihood framework. All viruses belonged to a separate subgroup (termed "EMA-3") within clade 2.2, and, thus, were distinct from two lineages of HPAIV H5N1 viruses (termed "EMA-1" and "EMA-2") present in the same geographic area in 2006. Analysis of concatenated coding regions of all eight genome segments significantly improved resolution and robustness of the reconstructed phylogenies as compared to single gene analyses. At the same time, the methodological limits to establish retrospectively transmission networks in a comparatively small geographic region and spanning a short period of time became evident when only few corroborating field-epidemiological data are available. Ambiguities remained concerning the origin of the EMA-3 viruses from a region covering Southeast Germany and the Czech Republic as well as routes of spread to other European countries. AIV monitoring programmes in place for wild birds and poultry in these countries did not reveal presence of these viruses in either population. Host switches between domestic poultry and wild bird populations occurred several times. Analysis of outbreaks in Northeast Germany and nearby Northern Poland in December 2007 demonstrated that geographic and even temporal vicinity of outbreaks does not necessarily indicate a common source of incursion.