Understanding animal health threats from emerging H5 high pathogenicity avian influenza viruses
Lead Research Organisation:
University of Edinburgh
Department Name: Roslin Institute
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.
Organisations
- University of Edinburgh (Lead Research Organisation)
- Department for Environment Food and Rural Affairs (Co-funder)
- Animal and Plant Health Agency (Collaboration)
- Moredun Research Institute (Collaboration)
- James Hutton Institute (Collaboration)
- UNIVERSITY OF GLASGOW (Collaboration)
- THE PIRBRIGHT INSTITUTE (Collaboration)
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES) (Collaboration)
- Scotland's Rural College (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- Biomathematics and Statistics Scotland (BioSS) (Collaboration)
| Description | The consortium was set up as an emergency response to the 2021 and ongoing avian influenza epizootic with the aim of bringing together a multidisciplinary team of UK experts to build capacity that would, in the longer term, build capacity to deal with one of the primary infectious disease threats facing the UK and that in the short term, might identify some quick mitigation strategies. The award has been running for 10 months and its major success has been to nucleate a team that is successfully working together and starting to identify causes and possible intervention strategies. |
| First Year Of Impact | 2023 |
| Sector | Agriculture, Food and Drink,Environment |
| Impact Types | Societal,Policy & public services |
| Description | Chair Defra commissioned report on Highly Pathogenic Avian Influenza |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Chair of Defra SAC-ED |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.gov.uk/government/organisations/science-advisory-council |
| Description | Defra SAC-ED sub sub group on highly pathogenic avian influenza |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Defra Scientific Advisory Committee on Emerging and Exotic Diseases (SAC-ED). |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Mitigation Fund |
| Amount | £7,700 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2023 |
| Description | APHA |
| Organisation | Animal and Plant Health Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The Flu-MAP consortium is an 8-partner team comprised of scientists from the Animal & Plant Health Agency, The Pirbright Institute, The Royal Veterinary College, Imperial College London, the University of Leeds, the University of Cambridge and the University of Nottingham, along with The Roslin Institute, University of Edinburgh. The Roslin team is made up of Professor Paul Digard (local PI and provides general influenza molecular virology expertise), Professor Lisa Boden (social science expertise), Professor Mark Bronsvoort (epidemiologist), Professor Rowland Kao (epidemiology and modelling), Professor Lonneke Vervelde (avian immunology) and Dr Samantha Lycett (phylodynamics and modelling). |
| Collaborator Contribution | APHA lead the consortium (Professor Ian Brown) and provide surveillance and animal challenge expertise. |
| Impact | The consortium is multidisciplinary |
| Start Year | 2022 |
| Description | Barclay group, Imperial College London |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | "Flu-MAP" (formal name "Understanding animal health threats from emerging H5 high pathogenicity avian influenza viruses" and code BB/X006123/1) is a BBSRC/Defra-funded Rapid Response award set up in response to the recent epidemic in Northern Europe of highly pathogenic avian influenza in wild and domestic birds. The aim of the consortium funded by this award is to establish an interdisciplinary consortium with the expertise to provide research-led responses and mitigation to the current crisis. The two UK/University of Edinburgh PIs on the US-UK BBSRC-NIFA collaboration award are part of Flu-MAP involved in supplying broadly the same areas of expertise: molecular influenza virology (Professor Paul Digard, local lead PI), qualitative research expertise (Professor Lisa Boden), phylodynamics and epidemiology (Dr Samantha Lycett) and avian immunology (Professor Lonneke Vervelde). For this particular collaboration within Flu-MAP, the Digard group is working with the Barclay group to perform functional tests of the internal genes from the current H5 HPAIV epizootic viruses. |
| Collaborator Contribution | Professor Barclay's group are sharing plasmids, other reagents and expertise with us. |
| Impact | No outcomes yet - the collaboration has been running for less than a year |
| Start Year | 2022 |
| Description | Collaboration ANSES |
| Organisation | French Agency for Food, Environmental and Occupational Health & Safety (ANSES) |
| Country | France |
| Sector | Public |
| PI Contribution | My research team will work in the ANSES laboratories to set up organotypic avian cultures (intestinal organoids) of chicken, turkey and Guinea fowl which will be a unique opportunity. The organoids will then be infected with a variety of coronaviruses and avian influenza viruses (low and high pathogenic) and the viral replication will be analysed at different time points post infection. The RNA will be isolated and transported back to the UK to investigate the species specific immune responses using a high throughput qPCR array. The Roslin team will train the scientist at ANSES how to culture organoids whereas the team at ANSES will train the ECRs in virological techniques and working in a high containment laboratory. |
| Collaborator Contribution | The team at ANSES will contribute a lot of staff time, the animals, and will do the infection experiment in their high containment laboratory. In addition they will analyse the virus replication (RT-qPCR, egg titration and plaque assays) and we will write a joined publication describing the outcomes of this collaborative project. The data will feed in to many other projects related to avian corona and avian influenza viruses that are ongoing in the Vervelde group. |
| Impact | A collaborative project with ANSES, Ploufragan laboratory (reference lab for avian influenza), was initiated and funded by the BBSRC mitigation fund. This is a multidisciplinary collaboration in which the Roslin ECRs and PI will contribute their expertise in organotypic avian cultures (organoids) and the team at ANSES will contribute their virological expertise, the capacity to work with highly pathogenic avian influenza and their access to poultry species that we do not have in the U.K. (including guinea fowl, SPF turkeys and SPF ducks). The output of this collaboration will be joined peer reviewed publications on on host specific viral entry and immune responses (avian corona viruses and avian influenza viruses), preliminary data for follow on funding and future access to a wealth of virus strains and high containment laboratory and animal facilities. |
| Start Year | 2022 |
| Description | EPIC-IV Centre of Expertise on Animal Disease Outbreaks |
| Organisation | Biomathematics and Statistics Scotland (BioSS) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Prof Lisa Boden is a co-director of the EPIC Centre of Expertise (PI), and Dr Samantha Lycett co-leads Challenge 2 "Early Warning" (Co-I). We provide advice to the Scottish Government on animal disease outbreaks, including the avian influenza outbreaks in Scotland. Very specifically some of the phylodynamic modelling developed on this project has been used to help inform the avian influenza disease modelling of EPIC. |
| Collaborator Contribution | EPIC (Epidemiology, Population health and Infectious disease Control) is an ambitious animal health consortium project. EPIC is the Centre of Expertise on Animal Disease Outbreaks, bringing together Scottish-based expertise under one umbrella to best prepare Scotland's livestock industry and stakeholders for disease outbreaks. Specifically on avian influenza, the partners have contributed to the avian influenza epidemiological modelling effort and also collecting data from national and public sources on wild bird movements (for modelling). |
| Impact | Multi-disciplinary collaboration between Scottish Research Institutes and Higher Education Institutes for Centre of Expertise to inform Scottish Government about animal disease risks and to provide advice and analyses on epidemiology of animal diseases in Scotland. EPIC's multidisciplinary team include vets, mathematical modellers, environment scientists, social scientists and economists working together ensuring disease control is considered in a holistic way. |
| Start Year | 2022 |
| Description | EPIC-IV Centre of Expertise on Animal Disease Outbreaks |
| Organisation | James Hutton Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Prof Lisa Boden is a co-director of the EPIC Centre of Expertise (PI), and Dr Samantha Lycett co-leads Challenge 2 "Early Warning" (Co-I). We provide advice to the Scottish Government on animal disease outbreaks, including the avian influenza outbreaks in Scotland. Very specifically some of the phylodynamic modelling developed on this project has been used to help inform the avian influenza disease modelling of EPIC. |
| Collaborator Contribution | EPIC (Epidemiology, Population health and Infectious disease Control) is an ambitious animal health consortium project. EPIC is the Centre of Expertise on Animal Disease Outbreaks, bringing together Scottish-based expertise under one umbrella to best prepare Scotland's livestock industry and stakeholders for disease outbreaks. Specifically on avian influenza, the partners have contributed to the avian influenza epidemiological modelling effort and also collecting data from national and public sources on wild bird movements (for modelling). |
| Impact | Multi-disciplinary collaboration between Scottish Research Institutes and Higher Education Institutes for Centre of Expertise to inform Scottish Government about animal disease risks and to provide advice and analyses on epidemiology of animal diseases in Scotland. EPIC's multidisciplinary team include vets, mathematical modellers, environment scientists, social scientists and economists working together ensuring disease control is considered in a holistic way. |
| Start Year | 2022 |
| Description | EPIC-IV Centre of Expertise on Animal Disease Outbreaks |
| Organisation | Moredun Research Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Prof Lisa Boden is a co-director of the EPIC Centre of Expertise (PI), and Dr Samantha Lycett co-leads Challenge 2 "Early Warning" (Co-I). We provide advice to the Scottish Government on animal disease outbreaks, including the avian influenza outbreaks in Scotland. Very specifically some of the phylodynamic modelling developed on this project has been used to help inform the avian influenza disease modelling of EPIC. |
| Collaborator Contribution | EPIC (Epidemiology, Population health and Infectious disease Control) is an ambitious animal health consortium project. EPIC is the Centre of Expertise on Animal Disease Outbreaks, bringing together Scottish-based expertise under one umbrella to best prepare Scotland's livestock industry and stakeholders for disease outbreaks. Specifically on avian influenza, the partners have contributed to the avian influenza epidemiological modelling effort and also collecting data from national and public sources on wild bird movements (for modelling). |
| Impact | Multi-disciplinary collaboration between Scottish Research Institutes and Higher Education Institutes for Centre of Expertise to inform Scottish Government about animal disease risks and to provide advice and analyses on epidemiology of animal diseases in Scotland. EPIC's multidisciplinary team include vets, mathematical modellers, environment scientists, social scientists and economists working together ensuring disease control is considered in a holistic way. |
| Start Year | 2022 |
| Description | EPIC-IV Centre of Expertise on Animal Disease Outbreaks |
| Organisation | Scotland's Rural College |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Prof Lisa Boden is a co-director of the EPIC Centre of Expertise (PI), and Dr Samantha Lycett co-leads Challenge 2 "Early Warning" (Co-I). We provide advice to the Scottish Government on animal disease outbreaks, including the avian influenza outbreaks in Scotland. Very specifically some of the phylodynamic modelling developed on this project has been used to help inform the avian influenza disease modelling of EPIC. |
| Collaborator Contribution | EPIC (Epidemiology, Population health and Infectious disease Control) is an ambitious animal health consortium project. EPIC is the Centre of Expertise on Animal Disease Outbreaks, bringing together Scottish-based expertise under one umbrella to best prepare Scotland's livestock industry and stakeholders for disease outbreaks. Specifically on avian influenza, the partners have contributed to the avian influenza epidemiological modelling effort and also collecting data from national and public sources on wild bird movements (for modelling). |
| Impact | Multi-disciplinary collaboration between Scottish Research Institutes and Higher Education Institutes for Centre of Expertise to inform Scottish Government about animal disease risks and to provide advice and analyses on epidemiology of animal diseases in Scotland. EPIC's multidisciplinary team include vets, mathematical modellers, environment scientists, social scientists and economists working together ensuring disease control is considered in a holistic way. |
| Start Year | 2022 |
| Description | EPIC-IV Centre of Expertise on Animal Disease Outbreaks |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Prof Lisa Boden is a co-director of the EPIC Centre of Expertise (PI), and Dr Samantha Lycett co-leads Challenge 2 "Early Warning" (Co-I). We provide advice to the Scottish Government on animal disease outbreaks, including the avian influenza outbreaks in Scotland. Very specifically some of the phylodynamic modelling developed on this project has been used to help inform the avian influenza disease modelling of EPIC. |
| Collaborator Contribution | EPIC (Epidemiology, Population health and Infectious disease Control) is an ambitious animal health consortium project. EPIC is the Centre of Expertise on Animal Disease Outbreaks, bringing together Scottish-based expertise under one umbrella to best prepare Scotland's livestock industry and stakeholders for disease outbreaks. Specifically on avian influenza, the partners have contributed to the avian influenza epidemiological modelling effort and also collecting data from national and public sources on wild bird movements (for modelling). |
| Impact | Multi-disciplinary collaboration between Scottish Research Institutes and Higher Education Institutes for Centre of Expertise to inform Scottish Government about animal disease risks and to provide advice and analyses on epidemiology of animal diseases in Scotland. EPIC's multidisciplinary team include vets, mathematical modellers, environment scientists, social scientists and economists working together ensuring disease control is considered in a holistic way. |
| Start Year | 2022 |
| Description | Pirbright Institute |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | As BBSRC Institutes within the National Institutes of Bioscience umbrella we collaborate on a variety of virology projects, pooling expertise, facilities and data. |
| Collaborator Contribution | Please see the specific publications involving joint authors |
| Impact | Toward the aim of defining the basis of resistance of poultry to viral diseases (DO1.2), we analysed the early immune response of Brown Leghorn and inbred line 61 chickens housed by the National Avian Research Facility to infection by Infectious Bursal Disease Virus, in collaboration with The Pirbright Institute. This identified candidate genes and pathways associated with resistance (DOI: 10.1128/JVI.02828-14). Uplift funding totalling >£800k linking Pirbright and Roslin Institute researchers will use epitope fingerprinting to investigate the genetic plasticity of infectious bronchitis virus strains to develop improved cross-protective vaccines (BB/M012069/1). Toward making disease-resistant animals, research linking ISPG2 and ISPG4 aims to define the contribution of RelA polymorphism to resistance to African Swine Fever Virus in pigs. Challenge experiments at The Pirbright Institute are ongoing at the time of writing. We currently have two joint PhD students shared between the Institutes - one (Miss Anabel Clements, supervised by Professor Paul Digard [RI] and Drs Munir Iqbal and Holley Shelton [PI]) is working on virulence determinants of avian influenza virus, while the other (Miss Laura Dunn, supervised by Dr Pip Beard [RI] and Dr Linda Dixon [PI]) is studying miRNA modification by African swine fever virus. Dr Beard, a senior virologist and pathologist has been appointed to a joint Roslin / Pirbright position, starting 1st May, 2016. |
| Description | Interview with Financial Times over avian influenza |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A filmed interview with a journalist from the FT - the purpose to inform the newspaper's audience on the current outbreak of highly pathogenic avian influenza. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.youtube.com/watch?v=f-aHbL2mc_c |
| Description | Interview with Jeremy Howell of the BBC over avian influenza |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Interview with Jeremy Howell of the BBC over avian influenza - parts ended up in an online BBC article and on YouTube - https://www.youtube.com/watch?v=f-aHbL2mc_c |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.bbc.co.uk/news/science-environment-63464065 |
| Description | Interview with journalist from Time Magazine about Avian influenza |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Interview with journalist from Time magazine about the H5N1/X avian influenza outbreaks worldwide including North America and recent mammalian spill over events. Article is here: https://time.com/6254312/avian-flu-pandemic-mutations/ "Bird Flu Isn't a Danger to Humans...Yet" |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://time.com/6254312/avian-flu-pandemic-mutations/ |
| Description | Interview with the Financial Times over avian influenza |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Interview with Anjana Ahuja of the Financial Times over avian influenza. This led to quotes in a written article and a follow-up filming visit. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://enterprise-sharing.ft.com/redeem/53cb2981-8411-4a92-9049-9dd62921ca84 |
| Description | Interview with the Guardian newspaper over avian influenza |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | An interview with several follow up points with Phoebe Weston of the Grauniad newspaper over avian influenza, leading to a quote in one of her articles |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.theguardian.com/environment/2022/jul/20/avian-flu-h5n1-wreaks-devastation-seabirds-aoe |
| Description | Panelist for Science Media Centre media briefing event on avian influenza |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Panelist alongside the UK Chief Veterinary Officer and an Animal & Plant Health Agency representative for a media-briefing press conference on the subject of avian influenza. At least one clip was used on the Radio 4 Today programme (18/10/2022) |
| Year(s) Of Engagement Activity | 2022 |