Influenza virus A/H1N1, which is currently causing a pandemic, contains gene segments with ancestors in the North American and Eurasian swine lineages. To get insights into virus replication dynamics, clinical symptoms and virus transmission in pigs, we infected animals intranasally with influenza virus A/Regensburg/D6/09/H1N1. Virus excretion in the inoculated pigs was detected in nasal swabs from 1 day post-infection (p.i.) onwards and the pigs developed generally mild symptoms, including fever, sneezing, nasal discharge and diarrhoea. Contact pigs became infected, shed virus and developed clinical symptoms similar to those in the inoculated animals. Plasma samples of all animals remained negative for virus RNA. Nucleoprotein- and haemagglutinin H1-specific antibodies could be detected by ELISA 7 days p.i. CD4+ T cells became activated immediately after infection and both CD4+ and CD8+ T-cell populations expanded from 3 to 7 days p.i., coinciding with clinical signs. Contact chickens remained uninfected, as judged by the absence of virus excretion, clinical signs and seroconversion.

Avian influenza viruses (AIV) have been classified on the basis of 16 subtypes of hemagglutinin (HA) and 9 subtypes of neuraminidase. Here we describe genomic evidence for a new candidate HA subtype, nominally H19, with a large genetic distance to all previously described AIV subtypes, derived from a cloacal swab sample of a Common Pochard (Aythya ferina) in Kazakhstan, in 2008. Avian influenza monitoring in wild birds especially in migratory hotspots such as central Asia is an important approach to gain information about the circulation of known and novel influenza viruses. Genetically, the novel HA coding sequence exhibits only 68.2% nucleotide and 68.5% amino acid identity with its nearest relation in the H9 (N2) subtype. The new HA sequence should be considered in current genomic diagnostic AI assays to facilitate its detection and eventual isolation enabling further study and antigenic classification.

The potential role of wild birds as carriers of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 is still a matter of debate. Consecutive or simultaneous infections with different subtypes of influenza viruses of low pathogenicity (LPAIV) are very common in wild duck populations. To better understand the epidemiology and pathogenesis of HPAIV H5N1 infections in natural ecosystems, we investigated the influence of prior infection of mallards with homo- (H5N2) and heterosubtypic (H4N6) LPAIV on exposure to HPAIV H5N1. In mallards with homosubtypic immunity induced by LPAIV infection, clinical disease was absent and shedding of HPAIV from respiratory and intestinal tracts was grossly reduced compared to the heterosubtypic and control groups (mean GEC/100 µl at 3 dpi: 3.0×10² vs. 2.3×10⁴ vs. 8.7×10⁴; p<0.05). Heterosubtypic immunity induced by an H4N6 infection mediated a similar but less pronounced effect. We conclude that the epidemiology of HPAIV H5N1 in mallards and probably other aquatic wild bird species is massively influenced by interfering immunity induced by prior homo- and heterosubtypic LPAIV infections.

Despite considerable effort for surveillance of wild birds for avian influenza viruses (AIVs), empirical investigations of ecological drivers of AIV prevalence in wild birds are still scarce. Here we used a continental-scale dataset, collected in tropical wetlands of 15 African countries, to test the relative roles of a range of ecological factors on patterns of AIV prevalence in wildfowl. Seasonal and geographical variations in prevalence were positively related to the local density of the wildfowl community and to the wintering period of Eurasian migratory birds in Africa. The predominant influence of wildfowl density with no influence of climatic conditions suggests, in contrast to temperate regions, a predominant role for inter-individual transmission rather than transmission via long-lived virus persisting in the environment. Higher prevalences were found in Anas species than in non- Anas species even when we account for differences in their foraging behaviour (primarily dabbling or not) or their geographical origin (Eurasian or Afro-tropical), suggesting the existence of intrinsic differences between wildfowl taxonomic groups in receptivity to infection. Birds were found infected as often in oropharyngeal as in cloacal samples, but rarely for both types of sample concurrently, indicating that both respiratory and digestive tracts may be important for AIV replication.

A natural reassortant influenza A virus consisting of seven genome segments from pandemic (H1N1) 2009 virus and a neuraminidase segment from a Eurasian porcine H1N1 influenza A virus was detected in a pig herd in Germany. The obvious reassortment compatibility between the pandemic (H1N1) 2009 and H1N1 viruses of porcine origin raises concern as to whether swine may become a reservoir for further reassortants of pandemic (H1N1) 2009 viruses with unknown implications for human health and swine production.