Connecting the study of wild influenza with the potential for pandemic disease

Abstract

Continuing outbreaks of pathogenic (H5N1) and pandemic (SOIVH1N1) influenza have underscored the need to understand the origin, characteristics, and evolution of novel influenza A virus (IAV) variants that pose a threat to human health. In the last 4-5years, focus has been placed on the organization of large-scale surveillance programs to examine the phylogenetics of avian influenza virus (AIV) and host-virus relationships in domestic and wild animals. Here we review the current gaps in wild animal and environmental surveillance and the current understanding of genetic signatures in potentially pandemic strains.

Figure 1

Surveillance effort targeted towards wild birds. Anseriformes (ducks, geese, swans: green) and Charadriiformes (shorebirds, gulls, auks: blue) account for almost all samples from wild bird orders collected in North America and Europe. Data are based on number of samples (positive, negative & untested) deposited in Influenza Research Database at 20 September, 2012 (n = 152,312). Other sampled wild bird orders include: Ciconiiformes (storks, herons, egrets), Columbiiformes (doves, pigeons), Coraciiformes (kingfishers, bee-eaters, rollers, hornbills), Cuculiformes (cuckoos, roadrunners, Gruiformes (cranes, rails), Sphenisciformes (penguins), Passeriformes (perching birds), Pelicaniformes (pelicans), Piciformes (woodpeckers), Procellariiformes (albatrosses, shearwaters, petrels), Sphenisciformes (penguins).

Figure 2

Detection of IAV from environmental sources. Data represent counts of the thirteen hemagglutinin (HA) subtypes detected. Data are sourced from reports of environmental detection published in the literature and sequences available on Genbank.

Figure 3

Geographic distribution of IAV detected from the environment spans biomes and migratory flyways of wild birds. Sampling sites are indicated by a white circle.

Figure 4

Genomic segments involved in enhanced virulence and/or host switching. Segments carrying mutations that have been shown experimentally to be involved in such phenotypic changes are highlighted in solid black and discussed within the text. Most of the mutations recorded in viruses isolated from wild birds are related to spill over events of HPAI H5N1 from domestic birds. The fact that 6 segments are involved in mammalian adaptation reflects the complexity of this process and the bias towards studying IAV that switches to mammals.

Figure 5

Sample types from Anatidae (ducks, swans, geese) and Laridae (gulls, terns, kittiwakes) collected during global surveillance. Data are based on number of samples (positive, negative & untested) deposited in the Influenza Research Database at 20 September, 2012.