Abstract
Wild birds, particularly duck species, are the main reservoir of influenza A virus (IAV) in nature. However, knowledge of IAV infection dynamics in the wild bird reservoir, and the development of immune responses, are essentially absent. Importantly, a detailed understanding of how subtype diversity is generated and maintained is lacking. To address this, 18,679 samples from 7728 Mallard ducks captured between 2002 and 2009 at a single stopover site in Sweden were screened for IAV infections, and the resulting 1081 virus isolates were analyzed for patterns of immunity. We found support for development of homosubtypic hemagglutinin (HA) immunity during the peak of IAV infections in the fall. Moreover, re-infections with the same HA subtype and related prevalent HA subtypes were uncommon, suggesting the development of natural homosubtypic and heterosubtypic immunity (p-value = 0.02). Heterosubtypic immunity followed phylogenetic relatedness of HA subtypes, both at the level of HA clades (p-value = 0.04) and the level of HA groups (p-value = 0.05). In contrast, infection patterns did not support specific immunity for neuraminidase (NA) subtypes. For the H1 and H3 Clades, heterosubtypic immunity showed a clear temporal pattern and we estimated within-clade immunity to last at least 30 days. The strength and duration of heterosubtypic immunity has important implications for transmission dynamics of IAV in the natural reservoir, where immune escape and disruptive selection may increase HA antigenic variation and explain IAV subtype diversity.
Highlights
Influenza A viruses (IAVs) infect many different avian and mammalian hosts, including humans [1,2]
Author Summary Influenza A viruses (IAV) infect a range of hosts, with the largest diversity being found in waterfowl, dabbling ducks
IAVs exist in numerous antigenic subtypes that co-circulate
Summary
Influenza A viruses (IAVs) infect many different avian and mammalian hosts, including humans [1,2]. The largest viral genetic diversity and highest prevalence are found in species associated with wetlands [2]. Avian and mammalian influenza, including seasonal and pandemic flu in humans, are epidemiologically linked. The common view is that the genetic variation occurring in the wild bird reservoir can be seeded into other host species through de novo introductions, or through reassortment processes in animals permissive to both avian and mammalian-adapted viruses [3]. Given that the highest levels of IAV genetic variation are found in wild waterfowl, it is critical to understand evolution of the virus in these hosts
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