Selection Versus Mutation: Reducing the Risk of Vaccine Reversion
Lead Research Organisation:
The Pirbright Institute
Department Name: Avian Viral Diseases
Abstract
Vaccination against numerous endemic pathogens is an essential component of the poultry industry. Without these vaccines chickens would succumb to infection at an early age reducing the productivity of the industry well below sustainable levels. IBV is an endemic virus that causes severe disease outbreaks in chickens worldwide. Effective and economically viable vaccines against IBV are available and mainly produced from pathogenic virus strains by passing in eggs approximately one hundred times. During these passages the virus accumulates multiple sequence variations from the original pathogenic sequence. This ultimately leads to attenuation of the virus and the production of a live attenuated vaccine. These vaccines have lost their ability to cause disease but still elicit a protective immune response in the chicken, thus protecting the bird from future infections. However, as these are live viruses the potential for to revert back to a pathogenic form is considerable considering the few sequence changes between wild and vaccine strains.
Despite the importance of these vaccines to the poultry industry and the risk of reversion, the processes that occur and the selective forces that drive virus attenuation during egg passage are unknown. Importantly, the differential contribution of virus sequence mutation compared to the selection of minor variants already present in the virus population has not been determined. Understanding these basic processes is essential to the development of future vaccines to reduce the threat of reversion.
This study will use passaged pathogenic IBV strains produced in the same way as vaccines. In parallel we will use a unique system that allows us to passage a single virus clone rather than a mixed virus population. Using contemporary deep sequencing technology we will study the molecular changes that occur at fine resolution during the attenuation process. This will for the first time reveal how a mixed population of virus changes during vaccine manufacture and the extent to which individual viruses can mutate. These results will then inform a series of studies that manipulates the forces that drive virus change. The first will use IBV strains that contain a protein from another strain that influences the immune response in the chicken, and the second will use viruses that mutate much faster than wild type viruses. By passaging and deep sequencing these viruses in the same way as the wild type viruses, we will understand how different forces drive virus sequence mutation. These recombinant passaged viruses will then be tested to determine if this process has led to attenuation and also if they maintain the potential to infect other chickens that are exposed to vaccinated birds.
Ultimately this research will reveal how IBV is attenuated by egg passage and identify key regions of the genome that prevent the virus from causing disease but do not impair its potential as a vaccine. Moreover, we will further develop our understanding of how different pressures influence the attenuation process and potentially identify ways to improve the process of vaccine design by engineering attenuated viruses. By understanding and manipulating the processes that govern virus attenuation and vaccine production we aim to identify ways of reducing the danger of vaccine strains reverting and causing damaging disease outbreaks.
Despite the importance of these vaccines to the poultry industry and the risk of reversion, the processes that occur and the selective forces that drive virus attenuation during egg passage are unknown. Importantly, the differential contribution of virus sequence mutation compared to the selection of minor variants already present in the virus population has not been determined. Understanding these basic processes is essential to the development of future vaccines to reduce the threat of reversion.
This study will use passaged pathogenic IBV strains produced in the same way as vaccines. In parallel we will use a unique system that allows us to passage a single virus clone rather than a mixed virus population. Using contemporary deep sequencing technology we will study the molecular changes that occur at fine resolution during the attenuation process. This will for the first time reveal how a mixed population of virus changes during vaccine manufacture and the extent to which individual viruses can mutate. These results will then inform a series of studies that manipulates the forces that drive virus change. The first will use IBV strains that contain a protein from another strain that influences the immune response in the chicken, and the second will use viruses that mutate much faster than wild type viruses. By passaging and deep sequencing these viruses in the same way as the wild type viruses, we will understand how different forces drive virus sequence mutation. These recombinant passaged viruses will then be tested to determine if this process has led to attenuation and also if they maintain the potential to infect other chickens that are exposed to vaccinated birds.
Ultimately this research will reveal how IBV is attenuated by egg passage and identify key regions of the genome that prevent the virus from causing disease but do not impair its potential as a vaccine. Moreover, we will further develop our understanding of how different pressures influence the attenuation process and potentially identify ways to improve the process of vaccine design by engineering attenuated viruses. By understanding and manipulating the processes that govern virus attenuation and vaccine production we aim to identify ways of reducing the danger of vaccine strains reverting and causing damaging disease outbreaks.
Technical Summary
Avian coronavirus Infectious bronchitis virus (IBV) is responsible for an important disease affecting the global poultry industry; a potential threat to food security. Live attenuated vaccines are crucial for the protection of large commercial poultry flocks. IBV live attenuated vaccines are produced by multiple passage of a virulent virus in embryonated hens' eggs, an empirical process believed to result in spontaneous mutations resulting in attenuation. Viruses attenuated by this approach may only have a few mutations that are responsible for loss of virulence or the variation in mutations results in vaccines with differing effectiveness. A major drawback of the method is back-mutation and re-emergence of virulent virus. Recent work has shown that the number of mutations identified following attenuation results in a low number of amino acid substitutions, <20, in the whole genome. Other recent work has shown that coronaviruses, in contrast to other positive sense RNA viruses, encode a proof-reading activity as part of their replicase repertoire. This raises the possibility that attenuation of IBV may result from selection of minor variants present in the initial inoculum rather than the accumulation of spontaneous mutations.
This project presents a unique opportunity by combining two fundamental technologies, second generation deep sequencing and IBV reverse genetics, to understand, for the first time, the process of attenuation used to generate IBV vaccines. Knowledge gained will significantly help to reduce the possibility of reversion. Moreover, by decreasing the proofreading ability of IBV it may be possible to develop vaccine strains that elicit a protective immune response but are short lived as they will accrue too many mutations to survive in the environment. Reducing the chances of reversion and the danger that live attenuated IBV vaccines may be responsible for the emergence of new pathogenic variants as a result of recombination with field isolates.
This project presents a unique opportunity by combining two fundamental technologies, second generation deep sequencing and IBV reverse genetics, to understand, for the first time, the process of attenuation used to generate IBV vaccines. Knowledge gained will significantly help to reduce the possibility of reversion. Moreover, by decreasing the proofreading ability of IBV it may be possible to develop vaccine strains that elicit a protective immune response but are short lived as they will accrue too many mutations to survive in the environment. Reducing the chances of reversion and the danger that live attenuated IBV vaccines may be responsible for the emergence of new pathogenic variants as a result of recombination with field isolates.
Planned Impact
Poultry is an important food source worldwide, there are an estimated 55 billion chickens including 5 billion for egg production. Viral diseases are a constant threat to the poultry industry through loss or reduction in the production, decreases in egg production and quality and affects on animal welfare. IBV causes an acute highly contagious and economically important respiratory disease responsible for economic losses to poultry industries across the globe and is a threat to food security. IBV also affects both the production and quality of eggs and despite the availability of live and inactivated vaccines continues to be a major problem worldwide. Live attenuated vaccines are produced by multiple passages of virulent isolates in embryonated domestic fowl eggs. This procedure is empirical, the mechanism of attenuation is unknown, often a fine balance between attenuation and loss of immunogenicity and has the major drawback of reversion to virulence.
The ultimate aim of this proposal is to determine how multiple passages of the virus results in attenuation and to use the information gained for the development of safer IBV vaccines by reducing their ability to revert to virulence if they escape into the environment. There are several beneficiaries of the work planned in this project.
BBSRC: Food security is recognised as an important research priority in the BBSRC 2010-2015 Strategic Plan. Results from this proposal will provide crucial information on how vaccines used to control an important avian endemic pathogen are attenuated, and information for the development of safer and more efficient vaccines ensuring that poultry farming remains not only a secure food source but also increases the economic competitiveness of the UK.
Poultry industry: IBV is a major challenge both to the UK and global poultry industry. In the UK, poultry production in 2010 was 904 million broilers and 34.5 million layers producing 9.7 billion eggs. The UK poultry industry is more than 90% self sufficient and in 2010 contributed around £4 billion to the UK economy supporting 60,000 associated jobs. Improved efficiency of the industry, through continued protection against endemic diseases such as IBV and the development of more efficient and safer vaccines, particularly against new and continually emerging variants of IBV, will have positive knock-on benefits both socially and for the UK economy. A Defra-funded report estimated that IBV affects 22 million birds in the UK incurring an overall cost of £23 million. At present, the mechanistic events resulting in attenuation is poorly understood; research to understand the molecular basis for attenuation, as described in this project, will provide the information to produce more effective and safer vaccines. This will result in improvements in animal welfare, reduced losses to the poultry industry and to reduce risks to food security.
Vaccine companies: The IAH coronavirus group has established collaborations, including direct support, with several vaccines companies that have resulted in ongoing assessment of potential vaccine candidates. This project is supported by one of the top poultry vaccine companies, Pfizer Animal Health, by the provision of virus passages used to produce a vaccine against the newly emerged IBV QX variant. The data generated during this project will allow us to understand how IBV is attenuated for the generation of vaccines and provide information for the design of safer vaccines.
Academia and Training: Results with respect to how viruses diverge and evolve on serial passage, especially in the absence of proof reading with respect to coronaviruses will be of interest to the scientific community and will be published in peer reviewed journals and presented at national and international scientific meetings. The project will provide professional training to a post-doctoral scientist, especially relating to virology and bioinformatics in respect to deep sequence analysis.
The ultimate aim of this proposal is to determine how multiple passages of the virus results in attenuation and to use the information gained for the development of safer IBV vaccines by reducing their ability to revert to virulence if they escape into the environment. There are several beneficiaries of the work planned in this project.
BBSRC: Food security is recognised as an important research priority in the BBSRC 2010-2015 Strategic Plan. Results from this proposal will provide crucial information on how vaccines used to control an important avian endemic pathogen are attenuated, and information for the development of safer and more efficient vaccines ensuring that poultry farming remains not only a secure food source but also increases the economic competitiveness of the UK.
Poultry industry: IBV is a major challenge both to the UK and global poultry industry. In the UK, poultry production in 2010 was 904 million broilers and 34.5 million layers producing 9.7 billion eggs. The UK poultry industry is more than 90% self sufficient and in 2010 contributed around £4 billion to the UK economy supporting 60,000 associated jobs. Improved efficiency of the industry, through continued protection against endemic diseases such as IBV and the development of more efficient and safer vaccines, particularly against new and continually emerging variants of IBV, will have positive knock-on benefits both socially and for the UK economy. A Defra-funded report estimated that IBV affects 22 million birds in the UK incurring an overall cost of £23 million. At present, the mechanistic events resulting in attenuation is poorly understood; research to understand the molecular basis for attenuation, as described in this project, will provide the information to produce more effective and safer vaccines. This will result in improvements in animal welfare, reduced losses to the poultry industry and to reduce risks to food security.
Vaccine companies: The IAH coronavirus group has established collaborations, including direct support, with several vaccines companies that have resulted in ongoing assessment of potential vaccine candidates. This project is supported by one of the top poultry vaccine companies, Pfizer Animal Health, by the provision of virus passages used to produce a vaccine against the newly emerged IBV QX variant. The data generated during this project will allow us to understand how IBV is attenuated for the generation of vaccines and provide information for the design of safer vaccines.
Academia and Training: Results with respect to how viruses diverge and evolve on serial passage, especially in the absence of proof reading with respect to coronaviruses will be of interest to the scientific community and will be published in peer reviewed journals and presented at national and international scientific meetings. The project will provide professional training to a post-doctoral scientist, especially relating to virology and bioinformatics in respect to deep sequence analysis.
Publications
Ferretti L
(2019)
SiNPle: Fast and Sensitive Variant Calling for Deep Sequencing Data
in Genes
FREIMANIS G
(2016)
Genomics and outbreaks: foot and mouth disease -EN- -FR- La génomique et le contrôle des foyers : la fièvre aphteuse -ES- Genómica y brotes: fiebre aftosa
in Revue Scientifique et Technique de l'OIE
Freimanis GL
(2020)
Whole-Genome Sequencing Protocols for IBV and Other Coronaviruses Using High-Throughput Sequencing.
in Methods in molecular biology (Clifton, N.J.)
Keep S
(2020)
Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus.
in The Journal of general virology
Keep SM
(2015)
Transient dominant selection for the modification and generation of recombinant infectious bronchitis coronaviruses.
in Methods in molecular biology (Clifton, N.J.)
Keep SM
(2015)
Partial purification of IBV and subsequent isolation of viral RNA for next-generation sequencing.
in Methods in molecular biology (Clifton, N.J.)
Maier HJ
(2015)
Preface. Coronaviruses.
in Methods in molecular biology (Clifton, N.J.)
Oade MS
(2019)
Attenuation of Infectious Bronchitis Virus in Eggs Results in Different Patterns of Genomic Variation across Multiple Replicates.
in Journal of virology
Description | We have developed a protocol to whole genome sequence Infectious Bronchitis viruses (a coronavirus), using high throughput sequencing technologies. The commercial QX Poulvax virus vaccine generation study (material provided by Zoetis) demonstrated that overall the virus had limited sequence variation compared to the original disease causing virus, with few new high frequency mutations observed across all egg passages. Overall, 9 changes were identified between the first passage and the commercial vaccine virus. Work is now ongoing to identify whether those 9 variants can be linked or increase the risk of reversion of virulence. A second virus (M41-CK) was serial passaged 100 times in eggs. This virus had greater diversity than QX, although exhibited just 1 shared mutation across all passages. Thirdly, the clone of M41-CK (M41-K) was unexpectedly found to have more variation than QX, but less than M41-CK. Overall, It exhibited 16 variants shared between all passages. Analysis has revealed the alternative and independent evolution of three infectious bronchitis viruses through the attenuation process of egg passage for producing live attenuated vaccines. We have evaluated the impact of factors, including selection and genetic bottlenecks during the attenuation process. Genetic bottlenecks appear to have large impacts upon the viral diversity in subsequent passages, with large bottlenecks severely restricting diversity, from which the viral populations do not always recover. The role of selection in the process of attenuation is weak, and possibly linked to the occurrence of these bottlenecks. Further to this, we identified that the 3 viruses passaged to attenuation reached their final attenuated state by different genetic pathways. Even related viruses i.e. M41-CK (wild type) and M41-K (a clone of wild type), were both attenuated with minimal numbers of intersecting/shared variants. This is now being prepared for publication and the methods have been used to underpin a follow on grant to reveal the error introduced through the process of NGS sequencing RNA viruses. Overall, although more work is required to understand if selection during attenuation can be identified through common signatures in viral sequence, this research has quantified how viral diversity during the process of attenuation and revealed multiple process behind the final vaccine seed. This is of great interest to coronaviruses more generally and also enables a better assessment of any vaccines potential to revert to virulence. |
Exploitation Route | Understanding the molecular basis for attenuation will allow us to rationally attenuate viruses for vaccine design. It will also allow us to develop better sequencing methods to monitor and track viral or viral vaccine evolution in field settings and potentially be part of the data needed to calculate risk of reversion. We have now submitted a grant proposal to the September 2020 BBSRC Responsive mode funding call that will act as a follow-on project and continue some of the work performed in this project, this includes several collaborators outside Pirbright. |
Sectors | Agriculture Food and Drink Pharmaceuticals and Medical Biotechnology |
Description | Training MSc students |
Geographic Reach | Local/Municipal/Regional |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | Delivered a new training session to MSc students teaching viral quantification assays. This lead to a greater understanding of laboratory techniques and academic research. |
Description | BBSRC responsive mode link award |
Amount | £1,382,000 (GBP) |
Funding ID | BB/P019137/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 02/2018 |
End | 01/2021 |
Description | Characterising Technical Biases in High Throughput Sequencing to Accurately Quantify RNA Viral Evolution |
Amount | £10,000 (GBP) |
Organisation | The Pirbright Institute |
Sector | Academic/University |
Country | United Kingdom |
Start | 11/2018 |
End | 03/2019 |
Description | Further development of infectious bronchitis virus vaccines adapted for production in cell culture |
Amount | £262,701 (GBP) |
Funding ID | BB/R019576/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2018 |
End | 03/2020 |
Description | Investigating Host and Viral Factors for Improved Design of Future Live Attenuated Vaccines for IBV |
Amount | £668,367 (GBP) |
Organisation | The Pirbright Institute |
Sector | Academic/University |
Country | United Kingdom |
Start | 03/2022 |
End | 03/2025 |
Description | Taiwan Partnering Award |
Amount | £40,700 (GBP) |
Funding ID | BB/S020624/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start |
Description | UK International coronavirus network (UK-ICN) |
Amount | £510,207 (GBP) |
Funding ID | BB/W003287/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2021 |
End | 09/2025 |
Title | GF - Next Generation Sequencing Workflow |
Description | A pipeline for the generation of next generation sequencing data for whole genome sequencing of avian coronavirus samples has been developed |
Type Of Material | Technology assay or reagent |
Year Produced | 2018 |
Provided To Others? | No |
Impact | This pipeline will enable us to generate whole genome sequences for avian coronaviruses to enable us to study genetic evolution of Infectious Bronchitis virus through vaccine development. |
Title | NGS pipeline |
Description | A pipeline for generation of next generation sequencing data from avian coronavirus samples has been developed. |
Type Of Material | Technology assay or reagent |
Provided To Others? | No |
Impact | This pipeline will allow us to generate next generation sequencing data to study the evolution of infectious bronchitis virus through the vaccine development process. |
Title | Optimisation of chicken kidney cell culture preparation |
Description | We have optimised the method of extracting kidneys and preparing chicken kidney (CK) cell cultures from chickens. CK cells are used for in vitro assays to study avian viruses, in particular infectious bronchitis virus. |
Type Of Material | Cell line |
Year Produced | 2017 |
Provided To Others? | No |
Impact | This has increased the yield of viable cells and the quality of the cell cultures. We can now obtain the number of cells we require using fewer chicken kidneys, therefore requiring fewer chickens to be culled. This is an important development for the 3Rs. We hope to publish this method for others' information. |
Title | GF - Next Generation Sequencing variant calling pipeline |
Description | This bioinformatics analysis pipeline enables us to identify low frequency variants in next generation sequencing datasets |
Type Of Material | Data analysis technique |
Year Produced | 2017 |
Provided To Others? | No |
Impact | This data will allow us to accurately identify low frequency variants within next generation sequencing datasets. These will be used to inform on future studies including improved vaccine design and advancing our understanding of molecular mechanisms underpinning attenuation during vaccine generation of RNA viruses including Infectious Bronchitis virus. |
Title | NGS data |
Description | IBV whole genome NGS datasets have been generated to compare pathogenic strains with those attenuated by serial passage in eggs. |
Type Of Material | Database/Collection of data |
Provided To Others? | No |
Impact | These datasets will allow us to determine the molecular basis for attenuation of IBV and will be used in the development of rationally attenuated live vaccines for the effective control of infectious bronchitis. |
Title | Spatial transcriptomics of Chicken trachea infected with Infectious bronchitis virus to identify transcriptomic signatures |
Description | Rhode Island Red SPF chickens were infected with M41-CK (a cell culture adapted pathogenic IBV virus) to investogate the evolution of the virus in chickens after infection, and compare with live attenuated vaccine versions of the same virus. Illumina sequence datasets were piped into the 10X proprietary analysis pipeline 'Space Ranger' for reads alignments, feature barcode matrices generation and secondary analysis including clustering and differential gene expression. Outputs from Space Ranger consisting of tissue images, tissue positions and feature barcode matrix were further piped into previously published R-based spatial pipeline 'Giotto' (Dries et al, 2021) for detailed analysis such as dimensionality reduction, co-visualization of gene expression and spatial location, cell type marker gene detection, spatial structure analysis, spatial gene co-expression patterns, etc. |
Type Of Material | Database/Collection of data |
Year Produced | 2024 |
Provided To Others? | No |
Impact | The dataset will have impact for other research groups investigating avian coronavirus vaccines. They will also have a broader impact and be of interest to wider coronavirus vaccine development and research thorough the information on vaccine evolution and host response. The datasets will be of interest to persons within the field of spatial biology field, notably the software developers and bioinformaticians, as a dataset to test new models and algorithms. The results will be of interest specifically for those in industry who are involved in developing novel and more rational strategies for developing vaccines. |
Description | Andrew Beck, ARC Mutation vs Selection |
Organisation | Centers for Disease Control and Prevention (CDC) |
Country | United States |
Sector | Public |
PI Contribution | We performed the experimental design and work and partial analysis of the results |
Collaborator Contribution | The partner has provided additional analysis techniques (intersection analysis between variants of inoculum and attenuated virus) in which they are specialists |
Impact | Paper currently being drafted for Genome Biology describing main findings of ARC Mutation vs Selection project |
Start Year | 2019 |
Description | Identification of conserved B-cell epitopes of highly pathogenic coronaviruses for broadspectrum immunotherapy and vaccine design. |
Organisation | Imperial College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have performed experiments to generate preliminary data for a collaborative grant application, contributed to the writing of the grant proposal and responded to reviewers comments. |
Collaborator Contribution | My collaborators have performed experiments to generate preliminary data for a collaborative grant application, contributed to the writing of the grant proposal and responded to reviewers comments. |
Impact | Submission of proposal entitled "Identification of conserved B-cell epitopes of highly pathogenic coronaviruses for broadspectrum immunotherapy and vaccine design" to the "One Health Approaches to Accelerate Vaccine Development" call that forms part of the UK government's commitment to Official Development Assistance (ODA) in October 2017. |
Start Year | 2017 |
Description | Identification of conserved B-cell epitopes of highly pathogenic coronaviruses for broadspectrum immunotherapy and vaccine design. |
Organisation | University of Kent |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have performed experiments to generate preliminary data for a collaborative grant application, contributed to the writing of the grant proposal and responded to reviewers comments. |
Collaborator Contribution | My collaborators have performed experiments to generate preliminary data for a collaborative grant application, contributed to the writing of the grant proposal and responded to reviewers comments. |
Impact | Submission of proposal entitled "Identification of conserved B-cell epitopes of highly pathogenic coronaviruses for broadspectrum immunotherapy and vaccine design" to the "One Health Approaches to Accelerate Vaccine Development" call that forms part of the UK government's commitment to Official Development Assistance (ODA) in October 2017. |
Start Year | 2017 |
Description | ARC final meeting 2017 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | This was the final project meeting for all ARC grants ending in this cycle where the final data was presented. |
Year(s) Of Engagement Activity | 2017 |
Description | Attended EPIZONE Workshop on Next Generation Sequencing applications and Bioinformatics, CODA-CERVA, Brussels (5th April - 8th April 2016) |
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 | Attended EPIZONE Workshop on Next Generation Sequencing applications and Bioinformatics, CODA-CERVA, Brussels (5th April - 8th April 2016) • "The workshop is aiming to provide a beginner's level introduction to Next Generation Sequencing technologies and NGS applications in veterinary virology, including data analysis and bioinformatics aspects" • Awarded EPIZONE Young Scientist Travel Grant, 500 EUR to support attendance |
Year(s) Of Engagement Activity | 2016 |
Description | BSI webinar |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | I presented a webinar hosted by the British Society for Immunology entitled "BSI Coronavirus webinar: What can we learn from the animal coronaviruses?", which sparked questions and discussions afterwards. I have since been contacted to establish new collaborations with people in the audience. |
Year(s) Of Engagement Activity | 2020 |
Description | Careers fair |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Students from several schools in the region attended the careers fair where we had a stall. Several students requested information about apprenticeships and were interested in possible careers in science. |
Year(s) Of Engagement Activity | 2011,2012,2013,2014,2015,2016,2017 |
Description | Centre of excellence for research on avian diseases (CERAD) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | I was invited to present my work at the UK-China Centre of excellence for research on avian diseases (CERAD) meeting attended by researchers from UK, China and Thailand. There was lots of discussion about the research and future directions, including potential collaborations. |
Year(s) Of Engagement Activity | 2017 |
Description | Focused Meeting 2018: Molecular Biology and Pathogenesis of Avian Viruses (Oxford) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Delivered oral presentation at the Focused Meeting 2018: Molecular Biology and Pathogenesis of Avian Viruses presenting work and finding to date. |
Year(s) Of Engagement Activity | 2018 |
Description | GF - Institute Internal seminar |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | Internal Seminar talk to peers to discuss and debate findings Title: "Making an attenuated vaccine virus: A preliminary analysis on IB QX virus" Dr Erica Bickerton presented the first 15 minutes outlining the initial findings from an earlier stage of the project involving testing recombinant IBV viruses in chickens. I talked for the final 15 minutes on the work I had completed on the project involving the findings on the attenuation of QX virus during repeated passage in eggs. The main purpose of this activity was to disseminate findings/results from part of the project to the audience of peers within the institute. This was intended to be a point for discussion for the results, and to stimulate discussion and awareness within the institute regarding the project and its findings. A question and answer discussion session also followed afterwards. |
Year(s) Of Engagement Activity | 2017,2018 |
Description | Graham Freimanis - Presentation at Epi-Seq workshop on Next Generation Sequencing Applications and Bioinformatics,5th-8th April, 2016, CODA-CERVA Belgium |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Graham Freimanis - Presentation at Epi-Seq workshop on Next Generation Sequencing Applications and Bioinformatics,5th-8th April, 2016, CODA-CERVA Veterinary and Agrochemical Research Center, Brussels, Belgium Presentation: A Finely Balanced Scale: A Brief Guide to NGS Sample Preparation |
Year(s) Of Engagement Activity | 2016 |
Description | Graham Freimanis - Presentation at Fourth ARC Dissemination meeting, 1st-2nd November, 2016 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Presentation title: Selection vs Mutation: Whole Genome Sequencing of IBV Opportunity to discuss best practice and to provide guidelines on how to set up protocols |
Year(s) Of Engagement Activity | 2016 |
Description | Graham Freimanis Training at NGS training school "Bioinformatics and Next Generation Sequencing: coronavirus workflows for data generation and analysis", 27th-28th October, 2016. |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Study participants or study members |
Results and Impact | Graham Freimanis Training at NGS training school "Bioinformatics and Next Generation Sequencing: coronavirus workflows for data generation and analysis", 27th-28th October, 2016. |
Year(s) Of Engagement Activity | 2016 |
Description | International Avian Respiratory Disease Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Michael presented his research at the 2018 International Avian Respiratory Disease Conference in the US to an audience of avian researchers and representatives form the poultry veterinary vaccine industry. This sparked discussion and potential future collaborations |
Year(s) Of Engagement Activity | 2018 |
Description | International Day of Women and Girls in Science |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | I gave a quote as a STEM ambassador about why I think it is important to make sure women and girls have the same opportunities in STEM. This was shared on social media to celebrate International Day of Women and Girls in Science, a UN-led initiative. |
Year(s) Of Engagement Activity | 2019 |
Description | International Women's Day video for social media |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Three team members were interviewed about their careers in science for International Women's Day. The videos were posted on Pirbright's website, Facebook and Twitter to celebrate what we love about working in science. |
Year(s) Of Engagement Activity | 2018 |
Description | Interview for national newspaper |
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 a journalist from The Telegraph about coronavirus replication and transmission. |
Year(s) Of Engagement Activity | 2020 |
Description | Interview with Associated Press |
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 a journalist from Associated Press about coronavirus research at The Pirbright Institute. |
Year(s) Of Engagement Activity | 2020 |
Description | Interview with BBC Radio Surrey |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Interview with journalists from BBC Radio Surrey on the breakfast show about coronavirus research at The Pirbright Institute. |
Year(s) Of Engagement Activity | 2020 |
Description | Interview with BuzzFeed News |
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 a journalist from BuzzFeed News about coronavirus research at The Pirbright Institute. |
Year(s) Of Engagement Activity | 2020 |
Description | Invited seminar speaker |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Other audiences |
Results and Impact | Erica Bickerton was invited to give a seminar at Imperial College London, which sparked questions and discussion afterwards. |
Year(s) Of Engagement Activity | 2017 |
Description | MSc student visit |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | I hosted several MSc students from University of Surrey, discussed avian research with them and demonstrated some laboratory techniques. The students gained an understanding of academic research and laboratory work. |
Year(s) Of Engagement Activity | 2018,2019 |
Description | Michael Oade Delivered brief project summary presentation NGS training school "Bioinformatics and Next Generation Sequencing: coronavirus workflows for data generation and analysis", CODA-CERVA, Brussels (27th - 28th October) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Michael Oade Delivered brief project summary presentation NGS training school "Bioinformatics and Next Generation Sequencing: coronavirus workflows for data generation and analysis", CODA-CERVA, Brussels (27th - 28th October) |
Year(s) Of Engagement Activity | 2016 |
Description | Michael Oade Presented poster at ARC Dissemination Event, Edinburgh (1st November - 2nd 2016) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | Presented poster and 3 slide summary entitled 'Developing rationally attenuated infectious bronchitis virus (IBV) using next-generation sequencing data' |
Year(s) Of Engagement Activity | 2016 |
Description | Michael Oade Presented poster at ARC Grant Meeting, Edinburgh (3rd - 4th February 2016) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | Presented poster at ARC Grant Meeting, Edinburgh (3rd - 4th February 2016) entitled 'Using next generation sequencing to investigate the mechanism of IBV attenuation' |
Year(s) Of Engagement Activity | 2016 |
Description | Michael Oade attended Microbiology Society Annual Conference, Arena and Convention Centre (ACC), Liverpool (21st - 24th March 2016) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | Attended Microbiology Society Annual Conference, Arena and Convention Centre (ACC), Liverpool (21st - 24th March 2016) • £360 travel grant awarded to support attendance |
Year(s) Of Engagement Activity | 2016 |
Description | Michael Oade gave presentation 9th International Symposium on Avian Corona and Pneumoviruses and Complicating Pathogens, Utrecht (Leusden), The Netherlands (21st - 24th June) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Michael Oade gave presentation 9th International Symposium on Avian Corona and Pneumoviruses and Complicating Pathogens, Utrecht (Leusden), The Netherlands (21st - 24th June) Gave presentation 'Using next generation sequencing to investigate the mechanism of IBV attenuation' |
Year(s) Of Engagement Activity | 2016 |
Description | Michael Oade had an abstract accepted for Microbiology Society Annual Conference, Edinburgh International Conference Centre (EICC) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | The Biotechnology Young Entrepreneurs Scheme (Biotechnology YES) is an innovative competition developed to raise awareness of the commercialisation of bioscience ideas among early career researchers. |
Year(s) Of Engagement Activity | 2016 |
Description | Michael Oade participated at 2nd Annual Training course on Viral Bioinformatics and Genomics, University of Glasgow (1st to 5th August) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | Michael Oade participated at 2nd Annual Training course on Viral Bioinformatics and Genomics, University of Glasgow (1st to 5th August) Attended a "series of lectures and practical exercises that directly address bioinformatic challenges posed by the current surge of sequence data, with a focus on viral data sets and analyses" |
Year(s) Of Engagement Activity | 2016 |
Description | Michael Oade presented at Glasgow-Pirbright Discussion Meeting, University of Glasgow (14th - 15th April 2016) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | Michael Oade presented at Glasgow-Pirbright Discussion Meeting, University of Glasgow (14th - 15th April 2016) Small meeting to promote future collaborations between Pirbright and Glasgow where UoG students had to give a presentation Gave presentation entitled 'Using next generation sequencing to investigate the mechanism of IBV attenuation' |
Year(s) Of Engagement Activity | 2016 |
Description | Microbiology Society Annual conference (UK) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Poster or oral presentation at Microbiology Society annual conference, a major international event. The participants included researchers from many different areas of science. This provides a platform to promote research to a wider audience as well as discuss the key findings with experts in my own field. |
Year(s) Of Engagement Activity | 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019 |
Description | Microbiology Society Avian Focus Meeting (UK) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | I gave a 15 minute oral presentation to an audience of around 80 people in 2016 and 2018. The audience consisted of researchers from many different scientific institutions from different areas of avian research. This was a great opportunity to present to experts in this field and gain novel insights into the project and the possible applications of my work. |
Year(s) Of Engagement Activity | 2016,2018 |
Description | Nidovirus symposium |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | I presented my work at the Nidovirus Symposium, which is held every three years and brings together researchers from industry and academia from many different countries. I had some interesting discussions with other researchers and built my network. |
Year(s) Of Engagement Activity | 2017 |
Description | Opening of The Biggs Avian Research Facility |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | We presented our research and spoke to guests attending the opening of the Biggs Avian Research Facility at Pirbright. Guests who attended included politicians and members of the public from the local area, eminent researchers from other institutions, and members of BBSRC. Guests reported that they felt much more informed about the work going on at Pirbright and were impressed by our facilities. |
Year(s) Of Engagement Activity | 2023 |
Description | Positive Strand Viruses Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | This was a poster presentation. There were several different poster sessions at the conference allowing a large selection of people to view each poster. The audience included world leaders in my research field and important names from groups all over the world. This gave me the opportunity to discuss my work with other scientists on a one to one basis, leading to generation of new ideas for future experiments and collaborations. |
Year(s) Of Engagement Activity | 2010,2013,2016,2019 |
Description | Presentation at American Society for Virology 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 to give a keynote talk on "Rational vaccine design for the avian coronavirus infectious bronchitis virus" at the ASV Satellite Symposium: Viral Pathogenesis and Prevention in Animals, discussed research and future plans with other researches in the field. |
Year(s) Of Engagement Activity | 2021 |
Description | Presentation at Global Alliance for Research on Avian Diseases Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Presentation of my research at the Global Alliance for Research on Avian Diseases Conference in Vietnam to approximately 80 conference participants resulted in discussions about future research directions. |
Year(s) Of Engagement Activity | 2018 |
Description | Presentation at RIVR meetings |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | Presentation of my research at Recently Independent Virology Researchers (RIVR) meetings in 2016, 2017, 2018, 2019 and 2020. I discussed my work and future collaborations with other virology researchers working in the UK. |
Year(s) Of Engagement Activity | 2016,2017,2018,2019,2020 |
Description | Presentation to BBSRC Executive Board |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Other audiences |
Results and Impact | I presented our research to the BBSRC Executive Board when they visited The Pirbright Institute in September 2018 and discussed the impacts of our work.. |
Year(s) Of Engagement Activity | 2018 |
Description | Presentations at Microbiology Society focused conference on Avian Infectious Diseases |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The Microbiology Society supported a focused meeting on avian infectious disease research, bringing together scientists from all over the world to discuss their research. We gave presentations on "Characterisation of the Infectious Bronchitis Virus E Protein for Rational Vaccine Design" and "Rational vaccine design for the avian coronavirus infectious bronchitis virus", received good feedback on our work and ideas for future research. |
Year(s) Of Engagement Activity | 2021 |
Description | Reverse genetics seminar (University of Surrey) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | A seminar was given based upon the reverse genetics system of infectious bronchitis virus. The audience was a group of 10 -15 MSc students from University of Surrey. The students were engaged, asked questions about the research and careers in science. We were asked to repeat the seminar for the next year's intake of students. |
Year(s) Of Engagement Activity | 2013,2014,2015,2016,2017,2018 |
Description | School visit (Compton, West Berkshire) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | The school visits included working with small groups of a-level biology students demonstrating a technique in the curriculum. They were encouraged to ask us questions about our work and how we use the technique as well as trying it out for themselves. |
Year(s) Of Engagement Activity | 2012,2013,2014,2015 |
Description | Teentech |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | The annual Teentech student science event in Guildford aims to encourage teenagers to consider science subjects and science careers. Our stand had considerable interest from the schoolchildren who were very enthusiastic. The event stimulated an increased interest in science and research. |
Year(s) Of Engagement Activity | 2016,2019 |
Description | organised workshops at Microbiology Society annual conferences 2014 - 2018 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | I co-organised virology division workshops on viral evolution and diversity and RNA viruses with colleagues from the virology division. The workshops were held at the annual Microbiology Society conferences in spring each year. Organisation involved selecting abstracts for oral or poster presentation, ordering the presentations and chairing the sessions. |
Year(s) Of Engagement Activity | 2015,2016,2017,2018 |