Understanding animal health threats from emerging H5 high pathogenicity avian influenza viruses
Lead Research Organisation:
ROYAL VETERINARY COLLEGE
Department Name: Pathobiology and Population Sciences
Abstract
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Technical Summary
The UK poultry industry is experiencing severe socio-economic damage and threats from high pathogenicity avian influenza viruses (HPAIVs) H5Nx of clade 2.3.4.4. These viruses pose zoonotic infections risks. The rapid evolution of these viruses is modulating their biological behaviour (epidemiology, host-range, transmission, and pathogenesis) in different avian species. To determine potential risks and improve controls against these emerging and re-emerging viruses requires a comprehensive knowledge base about the nature of prevailing viruses, and an integrated cross-disciplinary approach to studying virus ecology and epidemiology based on understanding virus/host interactions, and the genetic determinants of virulence, transmissibility and antigenicity in wild birds/poultry.
This project will investigate how contemporary H5Nx HPAIVs acquire adaptive changes to increase fitness within domestic and wild avian populations. We will define viral and host factors that potentially contribute to increased transmissibility, persistence, and pathogenicity in wild birds and those that enhance their potential to disseminate and manifest disease in poultry. Evolutionary changes drive virological, immunological and zoonotic infection potential of these viruses therefore, our understanding of environmental and molecular correlates required or associated with successful evolution, immune escape, dissemination and maintenance of HPAIVs via migratory populations of wild birds will be developed. Furthermore, we will define molecular markers for successful interspecies transmission and fitness in poultry with severe clinical outcomes. The will provide insights for assessing threats from new and emerging strains, enabling national and international agencies to design and execute contingencies as part of risk mitigation and disease control. This will provide vital information when considering how to invest scarce resources for surveillance design aimed at early warning of the threat.
This project will investigate how contemporary H5Nx HPAIVs acquire adaptive changes to increase fitness within domestic and wild avian populations. We will define viral and host factors that potentially contribute to increased transmissibility, persistence, and pathogenicity in wild birds and those that enhance their potential to disseminate and manifest disease in poultry. Evolutionary changes drive virological, immunological and zoonotic infection potential of these viruses therefore, our understanding of environmental and molecular correlates required or associated with successful evolution, immune escape, dissemination and maintenance of HPAIVs via migratory populations of wild birds will be developed. Furthermore, we will define molecular markers for successful interspecies transmission and fitness in poultry with severe clinical outcomes. The will provide insights for assessing threats from new and emerging strains, enabling national and international agencies to design and execute contingencies as part of risk mitigation and disease control. This will provide vital information when considering how to invest scarce resources for surveillance design aimed at early warning of the threat.
Publications
Hosseini P
(2025)
Qualitative studies on farm managers perception of risk from HPAIV and implementation of biosecurity measures on UK poultry farms.
in Preventive veterinary medicine
Vickers SH
(2024)
Utilizing citizen science data to rapidly assess changing associations between wild birds and avian influenza outbreaks in poultry.
in Proceedings. Biological sciences
| Description | The following key findings were obtained so far: - We investigated associations between weekly spatial abundance of 152 species of wild birds and High Pathogenic Avian Influenza (HPAI) poultry outbreaks. During autumn/winter, associations were generally strongest with waterbirds such as ducks and geese; however, we also found significant associations in groups such as non-native gamebirds and rapid change in species-specific associations over time. Our results demonstrate the value of citizen science to rapidly explore wild species as potential facilitators of disease incursions into well-monitored populations, especially in regions where viral surveillance in wild species is limited. This can be a critical step towards prioritizing targeted surveillance that could inform species-specific biosecurity measures. - We have conduced phylodynamic analysis of virus found in 127 domestic birds and 35 wild birds. We have provided preliminary evidence that most incursions are originated from wild birds, with only small evidence of lateral spread between farm was also obtained. - Findings of the qualitative interview with farmers showed that farms' use of biosecurity with respect to disinfection regimes and use of foot dips were both well cited and observed. Similarly, farm managers were all highly likely to refer to the use of farm-specific and shed-specific rubber boots, while also citing stricter requirements for visitors and delivery/maintenance. Biosecurity concerning the layout of the premises, fencing, access to changing rooms and the general age and maintenance of buildings and sheds required significant improvement across many farms. Additionally, farm managers expressed strong feelings of stress and anxiety in recent years, particularly those who had experienced an AI outbreak recently. We argue that factors such as risk perceptions, remits of control, feelings of responsibility and autonomy, and consequences on mental health, are all factors that can inform how farm managers respond to outbreaks and implement or sustain biosecurity on farms. A greater emphasis on providing regular and tailored training and educational resources for the industry would be beneficial as would further services focusing on reducing the burden on farmers' mental health. The findings highlights that the onus for improving biosecurity cannot remain solely with farm managers and workers. Further research exploring the role of other stakeholders in the industry would help bridge remaining gaps in our understanding of biosecurity implementation. |
| Exploitation Route | The results of the project were presented to the Avian Core Group in the UK and at international conferences. While it is still too early to determine the full impact, these findings are expected to influence both policy and industry practices. Additionally, the outcomes have paved the way for further research on the role and impact of biosecurity measures in poultry farms, conducted as part of the Flutrailmap project. |
| Sectors | Agriculture Food and Drink |
| Description | The findings are being used in subsequent projects, particularly the FluTRailmap project. They have generated important awareness and discussion on the role of wild bird distribution and dynamics in the transmission of HPAI to poultry farms, as well as on potential surveillance strategies to evaluate. Finding are being use for epidemiological modelling work which is currently undertaken by Roslin Institute. Analyses of biosecurity practices have also been communicated to industry and governments through the Avian Core Group and at the WOAH General Assembly. These discussions have highlighted the importance of key social barriers to effective biosecurity implementation, which need to be considered when developing industry protocols and guidelines. |
| First Year Of Impact | 2025 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic Policy & public services |
| Description | Dr. Sarah Hill was invited as expert to the 'Global consultation on highly pathogenic avian influenza (HPAI)' organized by FAO |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Contribution to new or improved professional practice |
| URL | https://www.fao.org/documents/card/en/c/cc7302en |
| Description | Ecology and biology of HPAIV H5 (Kappa-Flu) |
| Amount | £868,622 (GBP) |
| Funding ID | UKRI Reference Number: 10108315 |
| Organisation | United Kingdom Research and Innovation |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2023 |
| End | 05/2027 |
| Description | Flu:Trailmap |
| Amount | £598,975 (GBP) |
| Funding ID | BB/Y006992/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2024 |
| End | 05/2025 |
| Description | Ethnographic study on farmers' perceptions and implementation of biosecurity in poultry farms |
| Organisation | Animal and Plant Health Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | RVC is the work package leader and helped provide general coordination of this task. In addition, two RVC experience ethnographers worked closely with University of Cambridge to provide inputs on questionnaire design, overall methodology and provide support on qualitative analysis of the data and writing. RVC also facilitate access to poultry farms for the implementations of interviews. |
| Collaborator Contribution | University of Cambridge employ social science methods to investigate farmers' perceptions and implementation of biosecurity measures on case and non-case farms of various types (differing in region, production type, scale). They conducted semi-structured interviews with farmers and workers, allowing for in-depth discussion of farming practices and biosecurity, including associated challenges. Observations were conducted during farm visits, leading to rich data, including farmers' reported experiences and perceptions, and evidence of farm biosecurity investment and (mis)management. They carry out thematic analysis of the data. APHA is facilitated access to outbreak data for the selection of case farms to interview. |
| Impact | A publication has been made (https://doi.org/10.1016/j.prevetmed.2025.106445) |
| Start Year | 2022 |
| Description | Ethnographic study on farmers' perceptions and implementation of biosecurity in poultry farms |
| Organisation | University of Cambridge |
| Department | Department of Veterinary Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | RVC is the work package leader and helped provide general coordination of this task. In addition, two RVC experience ethnographers worked closely with University of Cambridge to provide inputs on questionnaire design, overall methodology and provide support on qualitative analysis of the data and writing. RVC also facilitate access to poultry farms for the implementations of interviews. |
| Collaborator Contribution | University of Cambridge employ social science methods to investigate farmers' perceptions and implementation of biosecurity measures on case and non-case farms of various types (differing in region, production type, scale). They conducted semi-structured interviews with farmers and workers, allowing for in-depth discussion of farming practices and biosecurity, including associated challenges. Observations were conducted during farm visits, leading to rich data, including farmers' reported experiences and perceptions, and evidence of farm biosecurity investment and (mis)management. They carry out thematic analysis of the data. APHA is facilitated access to outbreak data for the selection of case farms to interview. |
| Impact | A publication has been made (https://doi.org/10.1016/j.prevetmed.2025.106445) |
| Start Year | 2022 |
| Description | Network Analysis of poultry farm contact |
| Organisation | Animal and Plant Health Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | RVC is exploring possibility to conduct Network Analysis of industry contact to understand potential networks that can facilitate or prevent spread of HPAI. RVC employs a research assistant to conduct this task |
| Collaborator Contribution | APHA is collaborating with RVC by facilitating access to tracing investigations of infected premises that can be used to map networks. APHA is also facilitated contact with industry and discussion of methodology and results. Results are now complete and manuscript writing is in process. |
| Impact | A manuscript is currently in preparation |
| Start Year | 2022 |
| Description | Phylodynamic analysis of HPAI virus to assess lateral vs wild bird spread into poultry farms |
| Organisation | Animal and Plant Health Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | To infer the contribution of wild birds versus lateral spread to viral incursion in farms in the UK in 2021-22, phylodynamic models will be updated with additional UK sequence data (currently ~120 virus genomes). Should there be enough sequences available, these phylodynamic estimates of apparent rates of incursion (wild to domestic birds), and/or numbers, locations and times of estimated observed incursion events will also be used to inform simulation models. RVC employs a post-doctoral research fellow to carry out this work. |
| Collaborator Contribution | APHA and Roslin institute provides the genome sequence data needed for this work. APHA provides also the meta data required. |
| Impact | A total of 127 domestic birds genomes and 35 wild birds genomes were analyzed. Outputs indicate that most incursions into poultry farms were originated from wild bird incursions, but that evidence of farm-to-farm spread was also obtained for some farms. These findings are being investigated in further detail as part of FLU-TRAILMAP by collaborators at Roslin Institute. |
| Start Year | 2022 |
| Description | Phylodynamic analysis of HPAI virus to assess lateral vs wild bird spread into poultry farms |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | To infer the contribution of wild birds versus lateral spread to viral incursion in farms in the UK in 2021-22, phylodynamic models will be updated with additional UK sequence data (currently ~120 virus genomes). Should there be enough sequences available, these phylodynamic estimates of apparent rates of incursion (wild to domestic birds), and/or numbers, locations and times of estimated observed incursion events will also be used to inform simulation models. RVC employs a post-doctoral research fellow to carry out this work. |
| Collaborator Contribution | APHA and Roslin institute provides the genome sequence data needed for this work. APHA provides also the meta data required. |
| Impact | A total of 127 domestic birds genomes and 35 wild birds genomes were analyzed. Outputs indicate that most incursions into poultry farms were originated from wild bird incursions, but that evidence of farm-to-farm spread was also obtained for some farms. These findings are being investigated in further detail as part of FLU-TRAILMAP by collaborators at Roslin Institute. |
| Start Year | 2022 |
| Description | Phylogenetic analysis and epidemiological modelling of HPAI |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | RVC leads this workpackage and hence provide support in coordination of the project and communication with other partners. We (RVC) provide data and models on wild birds distribution in the UK which is used by our collaborators in Roslin institute to assess the genomic constallations that are linked to different flyways. This data and also data on industry Network analysis will be used to inform epidemiological models that can help predict HPAI outbreaks in the UK. |
| Collaborator Contribution | Our collaborators acquired wild bird movement data from RVC and combined it with available genome sequence data from the UK, and our European/international collaborators via GISAID, to make phylodynamic reconstructions from the 2020/21 and 2021/22 epizootic seasons. Phylodynamic reconstructions were performed per viral segment and enabled an assessment of which genome constellations (genotypes, i.e., segment combinations) are moved through different flyways. Viral sequence data from different bird species in Europe is available, although potentially under sampled and biased. The work attempt to estimate the contributions of different wild bird species to viral transmission patterns and maintenance in Europe and the UK from the viral sequence data and will assess the extent to which phylogenetically-reconstructed virus lineage movements are captured by, and predictable from host density and movement data, and environmental factors (e.g., temperature) using phylodynamic generalised linear models. The collaboration also involves comparisons between HPAI risk patterns in previous years, combined with inference from phylodynamic models, that will be used to estimate the relative roles of domestic and migratory waterfowl in terms of infection pressure on domesticated poultry, and therefore potential knock-on effects on lateral spread between farms. This will form the basis of simple spatial simulation models that will be used to predict possible burdens on poultry premises under summer conditions. Roslin institute has key expertise in phylodynamic and epidemiological analysis needed to carried out this task. |
| Impact | Results are still being produced, but initial understanding of genomic constellations and incursions of HPAI virus strain into the UK via wild birds have been generated. |
| Start Year | 2022 |
| Description | University of Leeds for the testing of wildfowl birds |
| Organisation | University of Leeds |
| Department | Faculty of Biological Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Dr. Alarcon (RVC) is the work package leader, under which this collaboration falls. I facilitate updates within the teams and presentation of findings to funders |
| Collaborator Contribution | The University of Leeds collaborated with wildfowlers association to take samples from shot ducks and geese during their standard hunting activities from late October 2022 to January 2022. Anseriform species were targeted with previous evidence of infection with H5Nx HPAIV during the 2021/22 season. The sampling of shot birds help define where subclinically infected birds may be shedding virus, thus potentially acting as a primary route of H5Nx HPAIV incursion into indigenous wild birds and poultry. Testing of birds were done on three sites, the Solway Firth, The Ribble and the Humble, selected because of well-established wildfowling clubs and evidence of infection in recent seasons. |
| Impact | A total of 810 samples have been tested, with 18 of these providing a positive result for High Pathogenic Avian Influenza. A manuscript was published (DOI: https://doi.org/10.1017/S0950268822001856) |
| Start Year | 2022 |
| Description | Poster presented at the Cambridge Infectious Diseases Annual Symposium (CID), Cambridge, UK, 4th March 2024. Poster title: Qualitative studies on farmers' perception of risk from HPAIV and implementation of biosecurity measures on UK poultry farms |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation |
| Year(s) Of Engagement Activity | 2024 |
| Description | Poster presented at the Conference of Research Workers in Animal Diseases (CRWAD), Chicago, USA, 20th - 23rd January 2024. Poster title: Qualitative studies on farmers' perception of risk from HPAIV and implementation of biosecurity measures on UK poultry farms |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation |
| Year(s) Of Engagement Activity | 2024 |
| Description | Poster presented at the Global Alliance for Research on Avian Diseases (GARAD) Conference, Surrey, UK, 22nd-24th May 2023. Poster title: Qualitative studies on farmers' perception of risk from HPAIV and implementation of biosecurity measures on UK poultry farms |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation |
| Year(s) Of Engagement Activity | 2023 |
| Description | Poster presented at the Society for Veterinary Epidemiology and Preventive Medicine (SVEPM) Conference, Uppsala, Sweden, 20th - 22nd March 2024. Poster title: Qualitative studies on farmers' perception of risk from HPAIV and implementation of biosecurity measures on UK poultry farms |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation of Flumap and Flutrail map findings and research activities and the UK-China Avian Flu Control Workshop and Flu-Trail Map Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The workshop aim at sharing research findings and awareness of research activities on avian influenza between UK (Flutrailmap project) and several Chinese institutions, including the reference laboratory for avian influenza. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation of study findings to the Avian Core Group in the UK - findings from the study " Qualitative studies on farmers' perception of risk from HPAIV and implementation of biosecurity measures on UK poultry farms" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation to high level stakeholders in the industry and government dealing with poultry |
| Year(s) Of Engagement Activity | 2023 |