Influenza A viruses: an ecology review

Abstract

In humans, influenza A viruses cause yearly outbreaks with high morbidity and excess fatality rates as a direct effect. Placed in its ecological niche, however – in dabbling ducks – avian influenza virus (AIV) induces quite a mild disease. It is when the virus crosses the species barrier that pathogenic traits are attributed to infection. When infecting phylogenetically more distant species (i.e. chicken and turkeys), the AIV can cause high morbidity and may in some cases change the virus into a highly pathogenic variant with nearly 100% fatality rate. Being a very adaptable virus, these spill-over events are frequent and numerous species are susceptible to influenza virus. When a subtype of AIV that has not previously infected humans crosses the species barrier, adapts to humans, and spreads easily, a pandemic event is imminent. There is no cure for influenza infection and vaccination is a cumbersome endeavor so, currently, the strategy when a pandemic strikes is damage control. The interest in AIV ecology has increased dramatically since the beginning of the millennium as a key factor for preventive work for future pandemics. This review gives a broad overview of influenza A virus ecology: in the natural host, accidental hosts, new endemic hosts, and humans.

Molecular epidemiology of swine influenza A viruses in the Southeastern United States, highlights regional differences in circulating strains

“…Waterfowl are the natural reservoir of IAVs; however, a wide range of species can be infected by IAVs such as domesticated poultry, humans, and swine (Ozawa and Kawaoka, 2013; Wahlgren, 2011). The zoonotic capability of IAVs and their potential to reassort have raised health concerns about IAVs emerging in animals and humans.…”

The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus

“…It would be interesting to use the analyses presented herein not only for a better understanding of virus evolution but also as supporting predictors of spill-over events, such as influenza (Wahlgren, 2011) and the new human coronavirus (Kindler et al, 2013) now named MERS-CoV, for which the role of codon usage evolution in virus adaptation to new hosts has been widely ignored.…”

Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation

“…However, both H3 and H1 have relatively large host ranges, with both successfully infecting wild birds, pigs and humans [34], suggest that they have similar conformational flexibility. Accordingly, dissimilarities between the minor alleles of the equine and swine studies are most likely a reflection of the immunological and physiological differences between the two host species [10,39].…”