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.
| Description | The following key findings were obtained so far: - We have developed models that predict weekly spatial abundance of 152 species of wild birds - 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, but evidence of lateral spread between farm was also obtained. |
| Exploitation Route | Manuscripts are being produced for submission in peer-review journals |
| Sectors | Agriculture, Food and Drink |
| Title | Wild birds abundance models for the UK |
| Description | We have extracted models of weekly predictive abundance of 152 wild birds species for the UK. Predictions are done for spatial units of 2.96 Km square. Changes in weekly abundance have been generated as a proxy for movements of wild birds. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | This models will allow assessing the potential predictive power of wild bird abundance to HPAI outbreaks in poultry farms, and which wild birds species are driving the outbreaks observed. |
| 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 helps provide general coordination of this task. In addition, two RVC experience ethnographers work closely with University of Cambridge to provide inputs on questionnaire design, overall methodology and provide support on qualitative analysis of the data. 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 will conduct semi-structured interviews with farmers and workers, allowing for in-depth discussion of farming practices and biosecurity, including associated challenges. Observations will be conducted during farm visits, leading to rich data, including farmers' reported experiences and perceptions, and evidence of farm biosecurity investment and (mis)management. They will carry out thematic analysis of the data. APHA is facilitating access to outbreak data for the selection of case farms to interview. APHA is also interested in developing a case-control study, and findings from this study will help inform possible future quantitative studies. Hence active discussions on collaborations are ongoing. |
| Impact | Interviews will commence in March 2023. Interview guide and protocol have been tested in 8 farms |
| 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 helps provide general coordination of this task. In addition, two RVC experience ethnographers work closely with University of Cambridge to provide inputs on questionnaire design, overall methodology and provide support on qualitative analysis of the data. 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 will conduct semi-structured interviews with farmers and workers, allowing for in-depth discussion of farming practices and biosecurity, including associated challenges. Observations will be conducted during farm visits, leading to rich data, including farmers' reported experiences and perceptions, and evidence of farm biosecurity investment and (mis)management. They will carry out thematic analysis of the data. APHA is facilitating access to outbreak data for the selection of case farms to interview. APHA is also interested in developing a case-control study, and findings from this study will help inform possible future quantitative studies. Hence active discussions on collaborations are ongoing. |
| Impact | Interviews will commence in March 2023. Interview guide and protocol have been tested in 8 farms |
| 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 facilitating contact with industry and discussion of methodology and results. |
| Impact | This work in currently ongoing |
| 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. Preliminary 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. |
| 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. Preliminary 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. |
| 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 |