Frequency and patterns of reassortment in natural influenza A virus infection in a reservoir host

- We investigated the frequency and patterns of reassortment of IAV in Mallards
- Of 92 viruses across 15 subtypes, 56% were estimated to be reassorted
- Negligible maintenance of segments or partial constellations across a season
- Patterns of reassortment differed between primary and secondary infections
- Infrequent viruses that do not occur annually are the product of reassortment

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.