title: Frequency and patterns of reassortment in natural influenza A virus infection in a reservoir host.
abstract: 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 of new 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.
authors.affiliation: Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar SE-391 82, Sweden.
authors.forename: Michelle
authors.initials: M
authors.lastname: Wille
authors.forename: Conny
authors.initials: C
authors.lastname: Tolf
authors.forename: Alexis
authors.initials: A
authors.lastname: Avril
authors.forename: Neus
authors.initials: N
authors.lastname: Latorre-Margalef
authors.forename: Sofie
authors.initials: S
authors.lastname: Wallerström
authors.forename: Björn
authors.initials: B
authors.lastname: Olsen
authors.forename: Jonas
authors.initials: J
authors.lastname: Waldenström
mesh_terms: D000818:Animals; D046090:Anseriformes / Q000821:virology*; D016000:Cluster Analysis; D060085:Coinfection / Q000821:virology; D004197:Disease Reservoirs; D019143:Evolution, Molecular; D005260:Female; D009980:Influenza A virus / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D016865:Reassortant Viruses / Q000235:genetics* / Q000302:isolation & purification; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral