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)
- Free University of Berlin (Collaboration)
- HyLine (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- James Hutton Institute (Collaboration)
- Purdue University (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
Publications
Aboah J
(2025)
Patterns of systemic problems in Ghana's poultry value chain: A group model building approach
in Journal of Agriculture and Food Research
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
Doeschl-Wilson A
(2023)
Evolutionary Dynamics of the Highly Recombinant Avian Coronavirus, Infectious Bronchitis Virus
in SSRN Electronic Journal
Douhard F
(2022)
The cost of host genetic resistance on body condition: Evidence from divergently selected sheep.
in Evolutionary applications
Ghaderi Zefreh M
(2023)
Exploring the value of genomic predictions to simultaneously improve production potential and resilience of farmed animals
in Frontiers in Genetics
Makau DN
(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
Osterrieder N
(2023)
Investigation of Gene Evolution and Phylodynamics in Marek's Disease Virus
in SSRN Electronic Journal
| Description | Four 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 four large-scale MDV transmission experiments, carried out by USDA-ADOL. In addition, a similar transmission experiment was carried out to assess the impact of vaccination on Infectious Bronchitis Virus transmission and evolution (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. A bioinformatic pipeline for processing Illumina short read sequences was developed at the Roslin Institute to investigate MDV polymorphisms in both consensus sequences and within mutant spectra (objective 2). Sequencing reads were firstly subjected to reference-based assembly to obtain the consensus, then remapped against this consensus to disclose minor variants. The procedure was subsequently validated using deep-sequencing reads generated from a historical collection of 60 pathotyped MDV strains. Using MCMC time-correlated phylogenetic analysis, we obtained substitution rates for the full genome, 46 diverse genes, and conserved genes. Effective population modelling and vaccine history integration identified genes potentially linked to vaccine es-cape across three vaccination periods. Genotype-phenotype associations revealed three previously un-linked pathogenicity genes. Molecular pathotyping using 4 SNVs from the Meq oncogene achieved 93% accuracy for 74% of strains, increasing to 92% accuracy overall by adding 3 SNVs from non-coding regions and pp14. Statistical analyses of the experimental data generated in objective 1 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. Mixed models assessed the effects of vaccination and host genetics on MD transmission. While vaccination (full and reduced dose) and genetic resistance did not prevent MDV infection, they significantly reduced MD pathology and death in vaccinated and resistant birds. Both vaccination and genetic resistance lowered MDV shedding, though the reduction was statistically significant only for full vaccination. Full-dose HVT vaccination also provided significant indirect protection to non-vaccinated contact birds by reducing MD disease, death, and virus shedding. Statistical path analysis revealed that these indirect effects were mediated by reduced FVL in infected birds (objective 3). To study vaccination and host genetics' effects on MDV infection and evolutionary dynamics (objective 3) , individual-based epidemiological models were developed alongside Bayesian inference methods to account for host resistance and infectivity variations. These methods are integrated into the software package BICI, which offers a flexible framework for fitting and modifying compartmental models. The models classify chickens as exposed ('E') and progressing through infectious states ('I1' to 'IN,' where N varies based on virus load). Bayesian inference estimates rates of progression or death. Data for low-dose vaccinated birds show vaccination significantly reduces disease progression, with fewer deaths in vaccinated birds. Mortality rates rise with disease severity, and few die in the 'E' state compared to many in the severe infection state. A notable finding was the impact of environmental pathogen burden, where higher initial MDV exposure accelerated disease progression. Overall, vaccination offers direct protection to vaccinated birds and indirect protection to the flock by reducing MDV shedding. Comparing estimated rates for individuals' disease progression across 10 passages so far provides no evidence for virus evolution towards increased transmissibility or virulence. The analyses are currently expanded to the other master datasets of this project. To assess the socio-economic burden of Marek's disease (objective 3) system dynamics (SD) models were developed by our partners from ILRI for small-scale poultry production in Ghana to assess how epidemiological and socio-economic factors affect farm and industry performance. A qualitative model iden-tified key intervention areas: research funding, biosecurity adoption, and reduced reliance on imported chicken. A quantitative SD model, combining disease epidemiology, financial analysis, and management decisions, evaluated disease mitigation strategies. Revaccination of locally hatched chicks reduced Marek's disease losses by over 76% in both systematic and cohort production schemes, while losses increased by 25.58% when using imported day-old chicks. Econometric analysis showed higher farm efficiency on farms that culled birds early during extreme weather or disease outbreaks and among older farmers. One study has been published, with two others in progress. |
| Exploitation Route | Our experimental and data informed modelling results provide relevant guidelines to poultry producers for controlling Marek's disease. Our experiments demonstrated that neither HVT vaccination with the full recommended or of highly reduced (1/10th) dose, nor host genetic resistance prevents MDV transmission. The ability to naturally transmit Marek's disease through 10 passages of vaccinated or genetically resistant birds highlights that unless the environment is deep cleaned, Marek's disease transmission will persist. Our results also indicate that vaccination effects may be underestimated. Vaccination 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. Genetic resistance does not seem to confer similar flock level protective effects. However, virus load in individual birds' feather follicles (FVL) was found to be a promising biomarker not only for individuals' shedding rate, but also for individuals' disease progression as well as for flock level protection. The results suggest that future control strategies should potentially aim at reducing FVL of individual birds. Future vaccine development and validation should assess the impact of vaccination on FVL. It has been highlighted to the poultry breeding company involved in the project that FVL may be a better phenotype for genetic selection for both, Marek's disease resistance and low infectivity of birds, thus offering flock level protection, and routes to take this forward are currently explored. The stakeholder workshops and decision support tools developed for chicken producers in Ghana enable poultry producers in Ghana and other countries to make more informed decisions about producing high health chicken. |
| 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 | Belgium |
| Start | 12/2022 |
| End | 11/2025 |
| Description | EUAqua.Org - Integrative breeding strategies for the transition of EUropean AQUAculture towards sustainable ORGanic productio |
| Amount | € 2,999,312 (EUR) |
| Funding ID | European Commission HORIZON-CL6-2024-BIODIV-01-9 grant, project ID 101181589 |
| Organisation | European Commission |
| Sector | Public |
| Country | Belgium |
| Start | 01/2025 |
| End | 12/2028 |
| Description | Prevention & Control of Infectious Diseases: Epidemiology and modelling |
| Amount | £583,602 (GBP) |
| Funding ID | BBS/E/RL/230002D |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2028 |
| Description | Prevention & Control of Infectious Diseases: Pathogen diversity and the basis of host-adaption and virulence |
| Amount | £1,069,853 (GBP) |
| Funding ID | BBS/E/RL/230002C |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2028 |
| Description | Prevention & Control of Infectious Diseases: Understanding the basis of host resistance |
| Amount | £502,785 (GBP) |
| Funding ID | BBS/E/RL/230002A |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2028 |
| 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 | 05/2022 |
| 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 | 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 | 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 | Diversity and Inclusion workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | Over 50 conference participants attended the Power Hour on Diversity and Inclusion in the Gordon Research Conference in Quantitative Genetics and Genomics. The group discussions provided a range of ideas and suggestions on how to improve diversity and inclusion in the academic workplace |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.grc.org/quantitative-genetics-and-genomics-conference/2025/ |
| Description | Diversity and Inclusion workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | Over 50 conference participants attended the Power Hour on Diversity and Inclusion in the Gordon Research Conference in Quantitative Genetics and Genomics. The group discussions provided a range of ideas and suggestions on how to improve diversity and inclusion in the academic workplace |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.grc.org/quantitative-genetics-and-genomics-conference/2025/ |
| 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 | Invited talk in international conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | The talk provided novel tools and results to assess the impact of host genetics in infectious disease transmission |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.grc.org/quantitative-genetics-and-genomics-conference/2025/ |
| Description | Invited talk in international conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | The talk provided novel tools and results to assess the impact of host genetics in infectious disease transmission |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.grc.org/quantitative-genetics-and-genomics-conference/2025/ |
| 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 | Presentation at international conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | 4 poster presentations were given at the Epidemics9 Conference in Bologna to demonstrate how vaccination or host genetics can affect transmission and evolutionary dynamics of important poultry viruses (Marek's disease and Infectious bronchitis virus) |
| Year(s) Of Engagement Activity | 2024 |
| 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/ |
| Description | stakeholder engagement worskhops |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Our ILRI partners held two main engagements with poultry sector stakeholders in Ghana: a stakeholder scoping meeting, and a (first) group model building workshop. The project approaches and updates were presented at both events, including a session presented (virtually) by the USDA partner. |
| Year(s) Of Engagement Activity | 2024 |