The epizootiology of avian influenza in wild birds and its risk to the UK poultry sector

The understanding of avian influenza and its associated risk in the UK has changed considerably over the last five years, with new foci species being identified, and changes in our understanding of viral prevalence throughout a calendar year. Concurrent with this changing of understanding, this thesis explored and challenged the known framework of what species spread avian influenza and how can we best monitor and mitigate against overspill into the UK poultry sector using a systematic literature review alongside field sampling and use of citizen science repositories to create exposure risk models. This thesis has identified that by increasing sample sizes above detection thresholds, the vast majority of species sampled sufficiently have evidence of the viral presence of avian influenza. Anatidae have been widely sampled within the literature due to their historic association with bird flu, and their presence within datasets looking at the importance of environmental variables skew results due to their high recorded avian influenza prevalence rates. Building upon this understanding led to the development of an alternative monitoring approach to the UK’s passive sampling method: active sampling via hunter-harvested waterfowl. Active sampling on a single site managed to confirm avian influenza in the UK before a national passive monitoring network, although this was discovered the following summer as testing was conducted retrospectively. The second half of the thesis focused on which species were present at two key habitats for avian influenza transmission, waterbodies, and poultry farms. Exposure risk models discovered that the family most sampled for avian influenza (Anatidae) were only recorded irregularly as a flyover to poultry holding sheds, though were universally present at Yorkshire’s waterbodies. The bird species found most regularly at and near poultry farms were mostly generalist passerines. The species most common at poultry farms weren’t the most common at waterbodies, but all bar one of the identified poultry farm target species were present across both key areas. This thesis presents an argument for wider sampling, a reflective look upon cost-effective monitoring techniques, and identifies the species representing the greatest exposure risk in wild bird communities at waterbodies and at Yorkshire poultry farms.