Investigating the Genetic Diversity of H5 Avian Influenza Viruses in the United Kingdom from 2020–2022

Publication history: Accepted - 27 April 2023; Published - 26 June 2023.Since 2020, the United Kingdom and Europe have experienced annual epizootics of high-pathogenicity avian influenza virus (HPAIV). The first epizootic, during the autumn/winter of 2020–2021, involved six H5Nx subtypes, although H5N8 HPAIV dominated in the United Kingdom. While genetic assessments of the H5N8 HPAIVs within the United Kingdom demonstrated relative homogeneity, there was a background of other genotypes circulating at a lower degree with different neuraminidase and internal genes. Following a small number of detections of H5N1 in wild birds over the summer of 2021, the autumn/winter of 2021–2022 saw another European H5 HPAIV epizootic that dwarfed the prior epizootic. This second epizootic was dominated almost exclusively by H5N1 HPAIV, although six distinct genotypes were defined. We have used genetic analysis to evaluate the emergence of different genotypes and proposed reassortment events that have been observed. The existing data suggest that the H5N1 viruses circulating in Europe during late 2020 continued to circulate in wild birds throughout 2021, with minimal adaptation, but then went on to reassort with AIVs in the wild bird population. We have undertaken an in-depth genetic assessment of H5 HPAIVs detected in the United Kingdom over two winter seasons and demonstrate the utility of in-depth genetic analyses in defining the diversity of H5 HPAIVs circulating in avian species, the potential for zoonotic risk, and whether incidents of lateral spread can be defined over independent incursions of infections from wild birds. This provides key supporting data for mitigation activities.This work was funded by the Department for Environment, Food, and Rural Affairs (Defra) (United Kingdom) and the Devolved Administrations of Scotland and Wales through the following programs of work: SV3400, SV3032, SV3006, and SE2213. Funding for diagnostic testing in Northern Ireland was provided by the Department for Agriculture, Environment, and Rural Affairs (DAERA). The writing and data analysis for the manuscript were also supported in part by the DELTA-FLU project funded by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 727922. A.C.B., J.J., and I.H.B. were also partly funded by the BBSRC/Defra-funded research initiative FluMAP (BB/X006204/1)