Investigating the genetic diversity of H5 avian influenza in the UK 2020-2022

Abstract

Since 2020, the UK and Europe, have experienced annual epizootics of high pathogenicity avian influenza virus (HPAIV). The first during autumn/winter 2020/21 involved the detected with six H5Nx subtypes although H5N8 HPAIV dominated in the UK. Whilst genetic assessment of the H5N8 HPAIVs within the UK 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 summer detections of H5N1 in wild birds over the summer of 2021, autumn/winter 2021/22 saw another European H5 HPAIV epizootic, that has 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 suggests that the H5N1 circulating in Europe during late 2020, continued to circulate in wild birds throughout 2021, with minimal adaptation, but has then gone on to reassort with AIVs in the wild bird population. We have undertaken an in-depth genetic assessment of H5 HPAIVs detected in the UK, over the last 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 incursion of infection from wild birds. Key supporting data for mitigation activities.

Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) from the 2021/22 epizootic is highly duck adapted and poorly adapted to chickens

“…In the 2020/21 autumn/winter season, the AI situation escalated considerably; the UK and European continent as whole experienced the largest HPAIV epizootic at the time, caused primarily by H5N8 HPAIV (H5N8-20) [7, 8]. Within this epizootic, four other H5 HPAIV subtypes (H5N1, H5N3, H5N4, H5N5), and at least 19 distinct genotypes were observed [8, 9].…”

“…In the 2020/21 autumn/winter season, the AI situation escalated considerably; the UK and European continent as whole experienced the largest HPAIV epizootic at the time, caused primarily by H5N8 HPAIV (H5N8-20) [7, 8]. Within this epizootic, four other H5 HPAIV subtypes (H5N1, H5N3, H5N4, H5N5), and at least 19 distinct genotypes were observed [8, 9]. The H5N1 subtype detected during this period contained the HA and M gene segment genetically related to the H5N8-20, but the remaining gene segments were likely donated from indigenous AIVs circulating in wild bird populations in Europe [8, 10].…”

“…Within this epizootic, four other H5 HPAIV subtypes (H5N1, H5N3, H5N4, H5N5), and at least 19 distinct genotypes were observed [8, 9]. The H5N1 subtype detected during this period contained the HA and M gene segment genetically related to the H5N8-20, but the remaining gene segments were likely donated from indigenous AIVs circulating in wild bird populations in Europe [8, 10]. A genetically highly related H5N1 was detected in a series of mass-die-off events in great skuas ( Stercorarius skua ) off the coast of Scotland during the summer of 2021 [11].…”

“…A genetically highly related H5N1 was detected in a series of mass-die-off events in great skuas ( Stercorarius skua ) off the coast of Scotland during the summer of 2021 [11]. The multi-subtype epidemiological scenario then changed during 2021/22 with the dominance of H5N1 HPAIV (H5N1-21), with only a small number of other subtypes (H5N2 and H5N8 [a single detection of H5N8 in a wild bird in 2021]) detected [8, 12]. In the UK, the 2021/22 epizootic began with H5N1 isolated from a chicken at a backyard poultry premise (IP) notified on the 24 th October 2021 [13].…”

“…In the UK, the 2021/22 epizootic began with H5N1 isolated from a chicken at a backyard poultry premise (IP) notified on the 24 th October 2021 [13]. This virus was an H5N1 HPAIV which shared high genetic similarity to the H5N1 circulating in wild birds at low levels in the previous 2020/21 epizootic [8, 10] and exhibited genetic drift which was evident during its persistence in UK wild birds during summer 2021 [11]. Since this first detection in poultry, there were over 145 confirmed IPs with HPAIV H5N1 in poultry and captive birds across Great Britain (GB) until the defined start of the 2022/23 epizootic on 1 st October 2022 [8, 13].…”