YY-EEID US-UK Collab: Combined influence of imperfect vaccines, host genetics, and non-genetic drivers on virus transmission and virulence evolution
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Summary (up to 4000 characters)
To maintain human and animal health, it is extremely important to understand how pathogens like viruses are transmitted and evolve to higher virulence. It is this knowledge that enables employment of effective and sustainable control strategies. Thus, it is necessary to collect, assemble, and analyse highly accurate datasets to determine the short- and long-term effectiveness of disease control approaches, that include biosecurity, genetic selection for disease resistance, and widespread vaccination. In this project, an international, interdisciplinary team investigates the impact of these approaches on the spread and evolution of two avian pathogenic viruses - Marek's disease virus (MDV) and infectious bronchitis virus (IBV) - both of which are primarily controlled by imperfect vaccines. It has been argued that imperfect vaccines like those to MDV and IBV, or host genetic resistance may alter the balance of selection between pathogen transmission and virulence by allowing a few more divergent but still virulent strains to be transmitted at reduced cost. However, these hypotheses have not been proven, and predictive frameworks are lacking for determining the combined influence of host and viral genetics, as well as vaccination on viral transmission and evolution to increased virulence. To address these knowledge gaps, a series of transmission experiments have been designed that utilize unique resources and data from 7,000+ birds under highly controlled conditions. In summary, the primary goal of this research is to collect informative, high-resolution empirical data and use these to build the next generation of data-informed mathematical models of virus transmission and evolutionary dynamics as a function of vaccination status, host genetics, and/or viral mutation rates. We will also address the important and possibly interdependent questions of genome variability and evolution towards increased virulence in vivo.
Besides the pure scientific merit of this research, we also strive towards lifting the project to high practical relevance. This requires a whole systems approach that also considers the broader socio-economic and political drivers of disease spread and virulence evolution. We will combine socio-economic studies with mathematical modelling to identify strategies for mitigating MD spread and MDV virulence evolution in sub-Saharan Africa, where poultry production is currently undergoing drastic increases in commercial production, similar to what was observed in the US in the 1960s.
We propose the following objectives to achieve scientific excellence and attain broader impact:
1. Determine the influence of imperfect vaccines, host genetics, and viral mutation rate on transmission and evolution to higher virulence.
2. Validate viral genome polymorphisms associated with increased virulence and the ability of the virus to escape immune surveillance.
3. Build data-informed evolutionary-epidemiological simulation models to develop strategies to control the ecology, evolution and economic burden of MD.
4. Disseminate information on MDV and IBV, and the impact of vaccination to poultry producers and the public through training, workshops, online videos, seminars, and various engagement activities
To maintain human and animal health, it is extremely important to understand how pathogens like viruses are transmitted and evolve to higher virulence. It is this knowledge that enables employment of effective and sustainable control strategies. Thus, it is necessary to collect, assemble, and analyse highly accurate datasets to determine the short- and long-term effectiveness of disease control approaches, that include biosecurity, genetic selection for disease resistance, and widespread vaccination. In this project, an international, interdisciplinary team investigates the impact of these approaches on the spread and evolution of two avian pathogenic viruses - Marek's disease virus (MDV) and infectious bronchitis virus (IBV) - both of which are primarily controlled by imperfect vaccines. It has been argued that imperfect vaccines like those to MDV and IBV, or host genetic resistance may alter the balance of selection between pathogen transmission and virulence by allowing a few more divergent but still virulent strains to be transmitted at reduced cost. However, these hypotheses have not been proven, and predictive frameworks are lacking for determining the combined influence of host and viral genetics, as well as vaccination on viral transmission and evolution to increased virulence. To address these knowledge gaps, a series of transmission experiments have been designed that utilize unique resources and data from 7,000+ birds under highly controlled conditions. In summary, the primary goal of this research is to collect informative, high-resolution empirical data and use these to build the next generation of data-informed mathematical models of virus transmission and evolutionary dynamics as a function of vaccination status, host genetics, and/or viral mutation rates. We will also address the important and possibly interdependent questions of genome variability and evolution towards increased virulence in vivo.
Besides the pure scientific merit of this research, we also strive towards lifting the project to high practical relevance. This requires a whole systems approach that also considers the broader socio-economic and political drivers of disease spread and virulence evolution. We will combine socio-economic studies with mathematical modelling to identify strategies for mitigating MD spread and MDV virulence evolution in sub-Saharan Africa, where poultry production is currently undergoing drastic increases in commercial production, similar to what was observed in the US in the 1960s.
We propose the following objectives to achieve scientific excellence and attain broader impact:
1. Determine the influence of imperfect vaccines, host genetics, and viral mutation rate on transmission and evolution to higher virulence.
2. Validate viral genome polymorphisms associated with increased virulence and the ability of the virus to escape immune surveillance.
3. Build data-informed evolutionary-epidemiological simulation models to develop strategies to control the ecology, evolution and economic burden of MD.
4. Disseminate information on MDV and IBV, and the impact of vaccination to poultry producers and the public through training, workshops, online videos, seminars, and various engagement activities
Technical Summary
Technical Summary (2000 chars)
In this project, an international, interdisciplinary team investigates the impact of vaccination and host and pathogen genetics, on the spread and evolution of two avian pathogenic viruses - Marek's disease virus (MDV) and infectious bronchitis virus (IBV) - both of which are primarily controlled by imperfect vaccines. It has been argued that imperfect vaccines like those to MDV and IBV, or host genetic resistance may alter the balance of selection between pathogen transmission and virulence by allowing a few more divergent but still virulent strains to be transmitted at reduced cost. However, these hypotheses have not been proven, and predictive frameworks are lacking for determining the combined influence of host and viral genetics, as well as vaccination on viral transmission and evolution to increased virulence. To address these knowledge gaps, a series of transmission experiments will be carried out that utilize unique resources and data from 7,000+ birds under highly controlled conditions. The primary goal of the proposed work is to generate informative, high-resolution empirical data and use these to establish the role of genome variability on virulence evolution, and to build the next generation of data-informed mathematical models to assess and predict the combined influence of genetics and vaccination on virus transmission and evolutionary dynamics. These models will be integrated into socio-economic systems models to develop strategies to control the ecology, evolution and economic burden of Mareks' disease. To maximise impact of the project results, the project also includes a comprehensive outreach programme.
In this project, an international, interdisciplinary team investigates the impact of vaccination and host and pathogen genetics, on the spread and evolution of two avian pathogenic viruses - Marek's disease virus (MDV) and infectious bronchitis virus (IBV) - both of which are primarily controlled by imperfect vaccines. It has been argued that imperfect vaccines like those to MDV and IBV, or host genetic resistance may alter the balance of selection between pathogen transmission and virulence by allowing a few more divergent but still virulent strains to be transmitted at reduced cost. However, these hypotheses have not been proven, and predictive frameworks are lacking for determining the combined influence of host and viral genetics, as well as vaccination on viral transmission and evolution to increased virulence. To address these knowledge gaps, a series of transmission experiments will be carried out that utilize unique resources and data from 7,000+ birds under highly controlled conditions. The primary goal of the proposed work is to generate informative, high-resolution empirical data and use these to establish the role of genome variability on virulence evolution, and to build the next generation of data-informed mathematical models to assess and predict the combined influence of genetics and vaccination on virus transmission and evolutionary dynamics. These models will be integrated into socio-economic systems models to develop strategies to control the ecology, evolution and economic burden of Mareks' disease. To maximise impact of the project results, the project also includes a comprehensive outreach programme.
Organisations
- University of Edinburgh (Lead Research Organisation)
- U.S. Department of Agriculture USDA (Collaboration)
- HyLine (Collaboration)
- James Hutton Institute (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
- Purdue University (Collaboration)
- Freie Universität Berlin (Collaboration)
Publications
Chase-Topping M
(2021)
Impact of vaccination and selective breeding on the transmission of Infectious salmon anemia virus
in Aquaculture
Doeschl-Wilson A
(2021)
Review: Livestock disease resilience: from individual to herd level.
in Animal : an international journal of animal bioscience
Douhard F
(2022)
The cost of host genetic resistance on body condition: Evidence from divergently selected sheep.
in Evolutionary applications
Makau D
(2022)
Ecological and evolutionary dynamics of multi-strain RNA viruses
in Nature Ecology & Evolution
Mucha S
(2022)
Animal Board Invited Review: Meta-analysis of genetic parameters for resilience and efficiency traits in goats and sheep.
in Animal : an international journal of animal bioscience
Petersen GEL
(2022)
Modeling suggests gene editing combined with vaccination could eliminate a persistent disease in livestock.
in Proceedings of the National Academy of Sciences of the United States of America
Pooley C
(2022)
Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission.
in Genetics, selection, evolution : GSE
| Description | Three high-resolution empirical datasets for detailed analyses of the effects of HVT vaccination and host genetics on Marek's disease virus (MDV) transmission and virulence evolution have been generated from three bespoke MDV transmission experiments, carried out by USDA-ADOL (Objective 1). These datasets are unique in their scope to (1) assess both the direct and indirect effects of vaccination or host genetic resistance to MD on the virus transmission, and to (2) monitor differences between vaccinated and non-vaccinated birds or birds that are genetically resistant / susceptible to MDV, with regards to changes in the virus sequences and associated changes in virulence over 10 successive generations (passages) of virus transmission between naturally infected shedder birds and naïve contact birds. Specifically, using inbred ADOL 15I5 x 71 antibody negative birds, Experiments 1 and 3 provided data from to determine to what extent vaccinations with the full recommended dose or 1/10 of the recommended dose of HVT, respectively, influences MDV transmission and viral genome evolution. Experiment 2 used outbred SPF layers Charles River line 22 and Babcock birds, known for their high and low resistance to MDV, respectively, to examine how host genetic resistance influences MDV transmission and evolutionary dynamics. Statistical analyses of the experimental data showed that the infection and transmission dynamics of birds that have been inoculated with MDV differ substantially from those of birds that have become naturally infected through contact with infected shedder birds, highlighting the importance of mimicking modes of transmissions representative of field conditions in vaccination and other MDV challenge experiments. Furthermore, experiment 1 demonstrated that HVT vaccination does not prevent MDV transmission within all 10 subsequent passages. However, vaccination with the full recommended HVT dose was found to not only provide direct protection from MD and death to the vaccinated birds, but also indirect protection for non-vaccinated contact birds. Preliminary analyses of experiment 1 data supports the hypotheses that MDV infection outcome of individual birds depends strongly on their exposure dose, that the latter decreases at a faster rate over successive generations of transmission in vaccinated or resistant birds and that feather virus load of infected shedder birds is a good indicator for their infectivity and, cumulatively, for the exposure dose of contact birds. The validity of these hypotheses will be further assessed using the data of all experiments combined, and with the use of epidemiological models. To this purpose, dynamic epidemiological and phylogenetic models have been developed to represent the experimental designs and the virus transmission and evolutionary dynamics (Objective 3). |
| Exploitation Route | The outcomes will inform poultry producers about the potential effects of imperfect vaccines on Marek's disease virus transmission and evolution. |
| Sectors | Agriculture, Food and Drink |
| Description | EU H2020 collaborative project ECO-READY- Achieving Ecological Resilient Dynamisms for the European food system through consumer-driven policies, socio-ecological challenges, biodiversity, data-driven policy, sustainable futures |
| Amount | € 14,948,450 (EUR) |
| Funding ID | 101084201 - ECO-READY |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 12/2022 |
| End | 11/2025 |
| Description | New social phenotypes from automated computer vision systems for reducing harmful social interactions and disease transmission in pigs through selective breeding |
| Amount | £54,900 (GBP) |
| Funding ID | BBSRC IAA PIII108 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2023 |
| End | 10/2023 |
| Description | TRAnsforming the DEbate about livestock systems transformation (TRADE) |
| Amount | £677,397 (GBP) |
| Funding ID | BB/W018152/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2022 |
| End | 05/2025 |
| Description | Research consortium EEID_US_UK Marek's Disease |
| Organisation | Free University of Berlin |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | In this project we aim to determine the impact of vaccination and host and pathogen genetics, on the spread and evolution of the Marek's disease virus (MDV). The spread of the virus and the impact of Marek's disease on the poultry industry is currently primarily controlled by imperfect vaccines and to a lesser extent through selective breeding. The project will generate high-resolution, empirical datasets to build the next generation of systems models incorporating host, viral, and management factors, as well as to establish the role of viral genome variability on virulence evolution. Using this data and epidemiological-evolutionary models we will then predict the combined influence of genetics, vaccination, and management practices on virus transmission, and assess the likely evolutionary dynamics in different socio-economic settings. In this first year, and in collaboration with our USDA partners, we have designed transmission experiments that produce empirical datasets to build the first generation of systems models for assessing vaccine and genetic effects on MDV transmission and evolutionary dynamics. Some data from the first experiment is now available from the partners, and statistical and mathematical modelling have begun. We are awaiting the production of within-sample variation viral sequence data from the first experiment (due in the first half of 2022), and in the meantime we have been developing the methodology to analyse similar deep sequencing viral data from prior experiments by the partners. For example, we are now able to assess the detailed within and between sample evolution, and estimate if there is evolutionary rate acceleration after the occurrence of key virulence enhancing mutations. |
| Collaborator Contribution | USDA has carried out 2 sets of transmission experiments to generate data for assessing vaccination and host genetic effects on MDV transmission and evolutionary dynamics. Disease and mortality data have been processed. qPCR analyses are currently carried out, and viral sequence data are currently generated. Partners from Free University of Berlin have provided deep sequence data from prior experiments and expertise to develop the phylodynamics methodology. Purdue University have started to develop educational material about poultry production and health targeted for elementary (primary) school children. ILRI's contribution to the project has been delayed due to delays in the collaboration agreement, but have started their development of the socio-economic models around poultry production and vaccination in Ghana. |
| Impact | A follow up collaborative project involving the USDA partners, as well as Dr. Guilherme Rosa from the University of Wisconsin, USA, entitled "Avian disease surveillance system for predicting transmission and evolution of pathogenic viruses in commercial poultry" has been submitted to the UKRI/BBSRC - NSF/BIO lead agency opportunity. The proposed project will build on the results from this current project to establish a first prototype of a poultry disease surveillance system" |
| Start Year | 2021 |
| Description | Research consortium EEID_US_UK Marek's Disease |
| Organisation | HyLine |
| Country | United States |
| Sector | Private |
| PI Contribution | In this project we aim to determine the impact of vaccination and host and pathogen genetics, on the spread and evolution of the Marek's disease virus (MDV). The spread of the virus and the impact of Marek's disease on the poultry industry is currently primarily controlled by imperfect vaccines and to a lesser extent through selective breeding. The project will generate high-resolution, empirical datasets to build the next generation of systems models incorporating host, viral, and management factors, as well as to establish the role of viral genome variability on virulence evolution. Using this data and epidemiological-evolutionary models we will then predict the combined influence of genetics, vaccination, and management practices on virus transmission, and assess the likely evolutionary dynamics in different socio-economic settings. In this first year, and in collaboration with our USDA partners, we have designed transmission experiments that produce empirical datasets to build the first generation of systems models for assessing vaccine and genetic effects on MDV transmission and evolutionary dynamics. Some data from the first experiment is now available from the partners, and statistical and mathematical modelling have begun. We are awaiting the production of within-sample variation viral sequence data from the first experiment (due in the first half of 2022), and in the meantime we have been developing the methodology to analyse similar deep sequencing viral data from prior experiments by the partners. For example, we are now able to assess the detailed within and between sample evolution, and estimate if there is evolutionary rate acceleration after the occurrence of key virulence enhancing mutations. |
| Collaborator Contribution | USDA has carried out 2 sets of transmission experiments to generate data for assessing vaccination and host genetic effects on MDV transmission and evolutionary dynamics. Disease and mortality data have been processed. qPCR analyses are currently carried out, and viral sequence data are currently generated. Partners from Free University of Berlin have provided deep sequence data from prior experiments and expertise to develop the phylodynamics methodology. Purdue University have started to develop educational material about poultry production and health targeted for elementary (primary) school children. ILRI's contribution to the project has been delayed due to delays in the collaboration agreement, but have started their development of the socio-economic models around poultry production and vaccination in Ghana. |
| Impact | A follow up collaborative project involving the USDA partners, as well as Dr. Guilherme Rosa from the University of Wisconsin, USA, entitled "Avian disease surveillance system for predicting transmission and evolution of pathogenic viruses in commercial poultry" has been submitted to the UKRI/BBSRC - NSF/BIO lead agency opportunity. The proposed project will build on the results from this current project to establish a first prototype of a poultry disease surveillance system" |
| Start Year | 2021 |
| Description | Research consortium EEID_US_UK Marek's Disease |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | In this project we aim to determine the impact of vaccination and host and pathogen genetics, on the spread and evolution of the Marek's disease virus (MDV). The spread of the virus and the impact of Marek's disease on the poultry industry is currently primarily controlled by imperfect vaccines and to a lesser extent through selective breeding. The project will generate high-resolution, empirical datasets to build the next generation of systems models incorporating host, viral, and management factors, as well as to establish the role of viral genome variability on virulence evolution. Using this data and epidemiological-evolutionary models we will then predict the combined influence of genetics, vaccination, and management practices on virus transmission, and assess the likely evolutionary dynamics in different socio-economic settings. In this first year, and in collaboration with our USDA partners, we have designed transmission experiments that produce empirical datasets to build the first generation of systems models for assessing vaccine and genetic effects on MDV transmission and evolutionary dynamics. Some data from the first experiment is now available from the partners, and statistical and mathematical modelling have begun. We are awaiting the production of within-sample variation viral sequence data from the first experiment (due in the first half of 2022), and in the meantime we have been developing the methodology to analyse similar deep sequencing viral data from prior experiments by the partners. For example, we are now able to assess the detailed within and between sample evolution, and estimate if there is evolutionary rate acceleration after the occurrence of key virulence enhancing mutations. |
| Collaborator Contribution | USDA has carried out 2 sets of transmission experiments to generate data for assessing vaccination and host genetic effects on MDV transmission and evolutionary dynamics. Disease and mortality data have been processed. qPCR analyses are currently carried out, and viral sequence data are currently generated. Partners from Free University of Berlin have provided deep sequence data from prior experiments and expertise to develop the phylodynamics methodology. Purdue University have started to develop educational material about poultry production and health targeted for elementary (primary) school children. ILRI's contribution to the project has been delayed due to delays in the collaboration agreement, but have started their development of the socio-economic models around poultry production and vaccination in Ghana. |
| Impact | A follow up collaborative project involving the USDA partners, as well as Dr. Guilherme Rosa from the University of Wisconsin, USA, entitled "Avian disease surveillance system for predicting transmission and evolution of pathogenic viruses in commercial poultry" has been submitted to the UKRI/BBSRC - NSF/BIO lead agency opportunity. The proposed project will build on the results from this current project to establish a first prototype of a poultry disease surveillance system" |
| Start Year | 2021 |
| Description | Research consortium EEID_US_UK Marek's Disease |
| Organisation | James Hutton Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | In this project we aim to determine the impact of vaccination and host and pathogen genetics, on the spread and evolution of the Marek's disease virus (MDV). The spread of the virus and the impact of Marek's disease on the poultry industry is currently primarily controlled by imperfect vaccines and to a lesser extent through selective breeding. The project will generate high-resolution, empirical datasets to build the next generation of systems models incorporating host, viral, and management factors, as well as to establish the role of viral genome variability on virulence evolution. Using this data and epidemiological-evolutionary models we will then predict the combined influence of genetics, vaccination, and management practices on virus transmission, and assess the likely evolutionary dynamics in different socio-economic settings. In this first year, and in collaboration with our USDA partners, we have designed transmission experiments that produce empirical datasets to build the first generation of systems models for assessing vaccine and genetic effects on MDV transmission and evolutionary dynamics. Some data from the first experiment is now available from the partners, and statistical and mathematical modelling have begun. We are awaiting the production of within-sample variation viral sequence data from the first experiment (due in the first half of 2022), and in the meantime we have been developing the methodology to analyse similar deep sequencing viral data from prior experiments by the partners. For example, we are now able to assess the detailed within and between sample evolution, and estimate if there is evolutionary rate acceleration after the occurrence of key virulence enhancing mutations. |
| Collaborator Contribution | USDA has carried out 2 sets of transmission experiments to generate data for assessing vaccination and host genetic effects on MDV transmission and evolutionary dynamics. Disease and mortality data have been processed. qPCR analyses are currently carried out, and viral sequence data are currently generated. Partners from Free University of Berlin have provided deep sequence data from prior experiments and expertise to develop the phylodynamics methodology. Purdue University have started to develop educational material about poultry production and health targeted for elementary (primary) school children. ILRI's contribution to the project has been delayed due to delays in the collaboration agreement, but have started their development of the socio-economic models around poultry production and vaccination in Ghana. |
| Impact | A follow up collaborative project involving the USDA partners, as well as Dr. Guilherme Rosa from the University of Wisconsin, USA, entitled "Avian disease surveillance system for predicting transmission and evolution of pathogenic viruses in commercial poultry" has been submitted to the UKRI/BBSRC - NSF/BIO lead agency opportunity. The proposed project will build on the results from this current project to establish a first prototype of a poultry disease surveillance system" |
| Start Year | 2021 |
| Description | Research consortium EEID_US_UK Marek's Disease |
| Organisation | Purdue University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | In this project we aim to determine the impact of vaccination and host and pathogen genetics, on the spread and evolution of the Marek's disease virus (MDV). The spread of the virus and the impact of Marek's disease on the poultry industry is currently primarily controlled by imperfect vaccines and to a lesser extent through selective breeding. The project will generate high-resolution, empirical datasets to build the next generation of systems models incorporating host, viral, and management factors, as well as to establish the role of viral genome variability on virulence evolution. Using this data and epidemiological-evolutionary models we will then predict the combined influence of genetics, vaccination, and management practices on virus transmission, and assess the likely evolutionary dynamics in different socio-economic settings. In this first year, and in collaboration with our USDA partners, we have designed transmission experiments that produce empirical datasets to build the first generation of systems models for assessing vaccine and genetic effects on MDV transmission and evolutionary dynamics. Some data from the first experiment is now available from the partners, and statistical and mathematical modelling have begun. We are awaiting the production of within-sample variation viral sequence data from the first experiment (due in the first half of 2022), and in the meantime we have been developing the methodology to analyse similar deep sequencing viral data from prior experiments by the partners. For example, we are now able to assess the detailed within and between sample evolution, and estimate if there is evolutionary rate acceleration after the occurrence of key virulence enhancing mutations. |
| Collaborator Contribution | USDA has carried out 2 sets of transmission experiments to generate data for assessing vaccination and host genetic effects on MDV transmission and evolutionary dynamics. Disease and mortality data have been processed. qPCR analyses are currently carried out, and viral sequence data are currently generated. Partners from Free University of Berlin have provided deep sequence data from prior experiments and expertise to develop the phylodynamics methodology. Purdue University have started to develop educational material about poultry production and health targeted for elementary (primary) school children. ILRI's contribution to the project has been delayed due to delays in the collaboration agreement, but have started their development of the socio-economic models around poultry production and vaccination in Ghana. |
| Impact | A follow up collaborative project involving the USDA partners, as well as Dr. Guilherme Rosa from the University of Wisconsin, USA, entitled "Avian disease surveillance system for predicting transmission and evolution of pathogenic viruses in commercial poultry" has been submitted to the UKRI/BBSRC - NSF/BIO lead agency opportunity. The proposed project will build on the results from this current project to establish a first prototype of a poultry disease surveillance system" |
| Start Year | 2021 |
| Description | Research consortium EEID_US_UK Marek's Disease |
| Organisation | U.S. Department of Agriculture USDA |
| Country | United States |
| Sector | Public |
| PI Contribution | In this project we aim to determine the impact of vaccination and host and pathogen genetics, on the spread and evolution of the Marek's disease virus (MDV). The spread of the virus and the impact of Marek's disease on the poultry industry is currently primarily controlled by imperfect vaccines and to a lesser extent through selective breeding. The project will generate high-resolution, empirical datasets to build the next generation of systems models incorporating host, viral, and management factors, as well as to establish the role of viral genome variability on virulence evolution. Using this data and epidemiological-evolutionary models we will then predict the combined influence of genetics, vaccination, and management practices on virus transmission, and assess the likely evolutionary dynamics in different socio-economic settings. In this first year, and in collaboration with our USDA partners, we have designed transmission experiments that produce empirical datasets to build the first generation of systems models for assessing vaccine and genetic effects on MDV transmission and evolutionary dynamics. Some data from the first experiment is now available from the partners, and statistical and mathematical modelling have begun. We are awaiting the production of within-sample variation viral sequence data from the first experiment (due in the first half of 2022), and in the meantime we have been developing the methodology to analyse similar deep sequencing viral data from prior experiments by the partners. For example, we are now able to assess the detailed within and between sample evolution, and estimate if there is evolutionary rate acceleration after the occurrence of key virulence enhancing mutations. |
| Collaborator Contribution | USDA has carried out 2 sets of transmission experiments to generate data for assessing vaccination and host genetic effects on MDV transmission and evolutionary dynamics. Disease and mortality data have been processed. qPCR analyses are currently carried out, and viral sequence data are currently generated. Partners from Free University of Berlin have provided deep sequence data from prior experiments and expertise to develop the phylodynamics methodology. Purdue University have started to develop educational material about poultry production and health targeted for elementary (primary) school children. ILRI's contribution to the project has been delayed due to delays in the collaboration agreement, but have started their development of the socio-economic models around poultry production and vaccination in Ghana. |
| Impact | A follow up collaborative project involving the USDA partners, as well as Dr. Guilherme Rosa from the University of Wisconsin, USA, entitled "Avian disease surveillance system for predicting transmission and evolution of pathogenic viruses in commercial poultry" has been submitted to the UKRI/BBSRC - NSF/BIO lead agency opportunity. The proposed project will build on the results from this current project to establish a first prototype of a poultry disease surveillance system" |
| Start Year | 2021 |
| Description | Discussion leader at a scientific conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion group leader of the "Health and Welfare Traits" session at the Quantitative Genetics and Genomics Gordon Research Conference, Ventura, February 2023. The session informed the audience about the state of the art of genomic approaches to human and animal health and welfare, and identified research gaps, and pathways to future implementation |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited talk at an international conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at the World Congress in Genetics Applied to Livestock Production (WCGALP) 2022 on "New tools and insights to enable breeding for reduced disease transmission. " The talk informed the audience about the latest approaches to reduce disease transmission in farm animals through selective breeding |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://doi.org/10.3920/978-90-8686-940-4_168 |
| Description | Lead Organiser of the BBSRC Cross Institute workshop on "The Future Role of Livestock in Food Production |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In this 2 day workshop, funded by the BBSRC, scientists and industry experts examined the need and scope for change in the livestock sector in response to increasing societal and environmental challenges. The outcome of the workshop resulted in a recommendation document sent to BBSRC that outlined the status quo and research and funding needs for future livestock research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ed.ac.uk/roslin/news-events/latest-news/future-of-livestock-production-in-the-spotlight |
| Description | Panellist at the live online University of Edinburgh: Changing World Conversations event, Nov 2022. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | This one hour virtual event was part of the University of Edinburgh's contribution to Cop26. I was one of three panel members. Our role was to inform the public about ongoing research in agriculture to mitigate the impact of climate change and to answer questions from members from the public. Many more questions were submitted by the public that could be addressed, showing the strong interest in the field. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.youtube.com/watch?v=vFiXTAz3vbM&list=PLBcSHVMkBQZgnM7t4LFMV11oEofR2J1vX&index=4 |
| Description | Participated as one of 4 panellists in the Science Media briefing event Can We Have Our Meat and Eat It? - The Future of Meat Production" Science Media Centre London 2019 |
| 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 | The briefing resulted in a wide media coverage in many regional and national newspapers, including the Guardian, The Sun, The Times etc.: Guardian https://www.theguardian.com/environment/2019/nov/28/gm-could-help-cut-livestock-methane-emissions-say-scientists PA via Hereford Times https://www.herefordtimes.com/news/national/18063917.breeding-help-cattle-become-environmentally-friendly-scientists-say/ Telegraph https://www.telegraph.co.uk/science/2019/11/27/meat-crucial-feeding-planet-going-vegan-not-green-say-scientists/ PA via iNews Clips Sky News https://news.sky.com/story/cattle-may-be-bred-to-grow-faster-and-eat-less-and-could-cut-methane-emissions-by-a-third-11871988 |
| Year(s) Of Engagement Activity | 2019 |
| Description | UKRI Climate change profile piece for Cop 26: |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | I was one of the University of Edinburgh's "climate pioneers" to contribute a short video clip describing how research on infectious disease in farm animals contributes to mitigating the impact of climate change on food security |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.ukri.org/our-work/responding-to-climate-change/our-climate-pioneers/ |