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Frequency and patterns of reassortment in natural influenza A virus infection in a reservoir host
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. (Zoonotic Ecology and Epidemiology)ORCID iD: 0000-0002-5629-0196
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. CIRAD, Campusinternational de Baillarguet, Montpellier 34398, France.
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
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2013 (English)In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 443, no 15, 150-160 p.Article in journal (Refereed) Published
Abstract [en]

Influenza A viruses (IAV) can dramatically alter both genotype and phenotype at a rapid rate as a product of co-infection and reassortment Avian IAV exhibit high levels of phylogenetic incongruence, suggesting high levels of reassortment in the virus reservoir. Using a natural-experimental system, we reconstructed relationships amongst 92 viruses across 15 subtypes from 10 Mallards in an autumn season. Phylogenetic analyses estimated that 56% of the isolated viruses were reassorted. Network analysis demonstrated different patterns of reassortment and limited exchange of segments between primary and secondary infections. No clear patterns of linkage between segments were found, and patterns within a season were likely the consequence of continued introduction ofnew constellations, high viral load and diversity in the wild bird reservoir, and co-infections. This is the first IAV study to implement multiple tools available for elucidating factors governing reassortment patterns in naturally infected Mallards.

Place, publisher, year, edition, pages
2013. Vol. 443, no 15, 150-160 p.
National Category
Research subject
Natural Science, Microbiology
URN: urn:nbn:se:lnu:diva-32897DOI: 10.1016/j.virol.2013.05.004ISI: 000322289900017OAI: diva2:705520
Available from: 2014-03-17 Created: 2014-03-17 Last updated: 2015-12-04Bibliographically approved
In thesis
1. Viruses on the wing: evolution and dynamics of influenza A virus in the Mallard reservoir
Open this publication in new window or tab >>Viruses on the wing: evolution and dynamics of influenza A virus in the Mallard reservoir
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis explores the evolution of avian influenza A viruses (IAV), as well as host-pathogen interactions between these viruses and their main reservoir host, the Mallard (Anas platyrhynchos). IAV is a genetically diverse, multi-host virus and wild birds, particularly dabbling ducks, are the natural reservoir. At our study site, up to 30% of migratory Mallards are infected with IAV during an autumn season, and host a large number of virus subtypes. IAV diversity is driven by two main mechanisms: mutation, driving genetic drift; and reassortment following co-infection, resulting in genetic shift.


Reassortment is pervasive within an autumn season, both across multiple subtypes and within a single subtype. It is a key genetic feature in long-term maintenance of common subtypes, as it allows for independent lineage turn-over, generating novel genetic constellations. I hypothesize that the decoupling of successful constellations and generation of novel annual constellations enables viruses to escape herd immunity; these genetic changes must confer antigenic change for the process to be favourable. Indeed, in an experiment utilizing vaccines, circulating viruses escaped homosubtypic immunity, resulting in the proliferation of infections with the same subtype as the vaccine. While the host plays an important role in shaping IAV evolutionary genetics, one must consider that Mallards are infected with a multitude of other microorganisms. Here, Mallards were infected with IAV, gamma coronaviruses, and avian paramyxovirus type 1 simultaneously, and we found a putative synergistic interaction between IAV and gamma coronaviruses.


Mallards occupy the interface between humans, poultry, and wild birds, and are the reservoir of IAV diversity. New incursions of highly pathogenic H5 viruses to both Europe and North America reaffirms the role of wild birds, particularly waterfowl, in diffusion of viruses spatially. Using European low pathogenic viruses and Mallard model, this thesis contributes to aspects of epidemiology, ecology, and evolutionary dynamics of waterfowl viruses, particularly IAV

Place, publisher, year, edition, pages
Växjö: Linnaeus University Press, 2015
Linnaeus University Dissertations, 217/2015
Co-infections, Ecology, Epidemiology, Evolution, Host-Parasite Interactions, Immunity, Influenza A Virus, Mallard, Phylogeny, Virology, Waterfowl, Wild Birds, Wildlife Disease
National Category
Research subject
Natural Science, Zoonotic Ecology
urn:nbn:se:lnu:diva-41431 (URN)978-91-87925-56-6 (ISBN)
Public defence
2015-05-08, Fullriggaren, Landgången 4, Kalmar, 09:30 (English)
Available from: 2015-03-27 Created: 2015-03-27 Last updated: 2015-12-04Bibliographically approved

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