Development of rationally attenuated live vaccines for effective control of infectious bronchitis

Lead Research Organisation: The Pirbright Institute
Department Name: UNLISTED

Abstract

The overall aim of this project is to attenuate the pathogenicity of infectious bronchitis virus (IBV) of poultry in a non-reversible way, whilst maintaining immunogenicity for both vaccination of chickens and for in ovo application. Control of infectious diseases and a reduction in the use of therapeutic antibiotics are two major challenges faced by the UK poultry industry. The avian coronavirus, IBV, is a highly contagious poultry pathogen prevalent in all types of poultry flocks worldwide. IBV is the causal agent of infectious bronchitis (IB) and continues to be responsible for economic loss, welfare problems in chickens and a potential risk to food security. IBV preferentially causes respiratory disease, but can also infect other organs such as the kidneys (resulting in kidney disease) or the reproductive tract (resulting in loss of egg production and/or egg quality). IBV has been reported to be responsible for more economic loss to the UK poultry industry than any other infectious disease. Although live attenuated vaccines and inactivated vaccines are universally used in the control of IBV, the protection gained by use of vaccination can be lost either due to vaccine breakdown or the introduction of a new IBV serotype that is not related to the vaccine used, posing a risk to the poultry industry. It is important that new and safer vaccines are developed for the control of IBV. This proposal seeks to develop an infectious clone system for the generation of rationally attenuated IBV vaccines, identifying two spatially distant regions of the genome that can be modified for attenuation. The project is divided into four main objectives:- 1) To produce an IBV reverse genetics system based on the pathogenic M41 strain of IBV. 2) To remove the M41 accessory non-structural genes to identify whether they play a role in pathogenicity. 3) To study the role of the M41 essential (replicase) non-structural protein genes in pathogenicity. 4) To investigate the attenuation of IBV for in ovo vaccination. This highly innovative project will be carried out by the coronavirus research group at the Institute for Animal Health, Compton which has the necessary IBV reverse genetics technology and the animal facilities to test rIBVs in chickens. The submission is in direct response to research requirements identified and agreed by the Poultry Research Committee at their meeting on the 17th November 2008. Expected benefits to the food chain: Relaxation of IBV vaccination strategies or the breakdown of vaccination, due to new IBV strains, would have a profound and devastating affect on the UK poultry industry in terms of bird welfare and production costs, with associated risks to food security. This work will pave the way for new rationally modified and safer vaccines, as they will be less likely to revert. A further expected benefit from the development of safer vaccines, is a reduction in the amount of antibiotics used to counteract secondary bacterial infections associated with IB.

Technical Summary

The overall aim of this project is to attenuate the pathogenicity of infectious bronchitis virus (IBV) of poultry in a non-reversible way, whilst maintaining immunogenicity for both vaccination of chickens and for in ovo application. Control of infectious diseases and a reduction in the use of therapeutic antibiotics are two major challenges faced by the UK poultry industry. The avian coronavirus, IBV, is a highly contagious poultry pathogen prevalent in all types of poultry flocks worldwide. IBV is the causal agent of infectious bronchitis (IB) and continues to be responsible for economic loss, welfare problems in chickens and a potential risk to food security. IBV preferentially causes respiratory disease, but can also infect other organs such as the kidneys (resulting in kidney disease) or the reproductive tract (resulting in loss of egg production and/or egg quality). IBV has been reported to be responsible for more economic loss to the UK poultry industry than any other infectious disease. Although live attenuated vaccines and inactivated vaccines are universally used in the control of IBV, the protection gained by use of vaccination can be lost either due to vaccine breakdown or the introduction of a new IBV serotype that is not related to the vaccine used, posing a risk to the poultry industry. It is important that new and safer vaccines are developed for the control of IBV. This proposal seeks to develop an infectious clone system for the generation of rationally attenuated IBV vaccines, identifying two spatially distant regions of the genome that can be modified for attenuation.

Planned Impact

Exploitation of the project outcomes: The submission is in direct response to research requirements identified and agreed by the Poultry Research Committee at their meeting on the 17th November 2008. The aims of the project also fulfil the Defra requirements for coronaviruses in poultry under 'Alternative pharmaceutical control of endemic animal diseases (Requirements 36-38)'. The IAH coronavirus group is the only research group in the UK that has the IBV reverse genetics system capable of modifying the IBV genome. At present there is only one other group in the world also using an IBV reverse genetics system. The work described in the proposal will benefit the poultry industry, not only from the development of safer vaccines but from benefits in terms of livestock husbandry, welfare and environmental impacts. The continuous use of IB vaccines to protect this important food source is responsible for keeping the impact of IBV on British poultry to a minimum. In the 2005 Defra report, IB was estimated to have affected 22.5 million chickens at a total cost of £23.6M (including £12.6M involving loss of egg production). Relaxation of vaccination strategies, or the breakdown of strategies by loss of protection due to new IBV strains, would have a profound and devastating affect on the UK poultry industry, in terms of welfare and economic cost. A major goal of the poultry industry is the development of an IBV vaccine that can be used for in ovo vaccination. The overall aim of the proposal is to identify suitable regions of the IBV genome that can be modified to attenuate a virulent IBV so that it may be developed as a basic vaccinial strain against different serotypes of IBV. It is unlikely that there will be direct commercialisation of the attenuated virus to be produced at the end of this project as it is at the developmental stage. The project will produce scientific information to underpin the development of a new generation of rationally attenuated IBV vaccines that are safer, have the potential to be modified for wider use against different serotypes and the possibility to be used for in ovo vaccination. This project is not directed towards the production of a formulation designed for an individual product. Subject to IP protection, results will be published in peer-reviewed scientific journals and presented at scientific meetings. The commercial partner, Pfizer Animal Health, is one of the few remaining major animal pharmaceutical companies. They produce a number of animal health vaccines and also support other work into basic and applied virology, with a direct interest in the development of vaccines against poultry diseases including IBV. They are therefore perfect partners to exploit outcomes from this work; for example, to investigate the development of rationally attenuated IBV vaccines that may be used in ovo. The support of an industrial partner will provide a bridge whereby promising vaccine candidates can be taken forward for commercial development. The information gained will be unique and of great value as to how IBV can be rationally attenuated and have a wider application than the development of a single product. Our previous work of spike swapping has demonstrated how IBV can be manipulated to afford protection over a wider range of IBV serotypes. I can foresee no problems why the attenuated virus from this project could not be manipulated in the same way.

Publications

10 25 50
 
Description A major objective of this project is to develop a reverse genetics system for the avian coronavirus, infectious bronchitis virus (IBV), based on the pathogenic M41 strain of IBV. We have generated such a system by the systematically adding and extending M41-derived sequence synthetically produced in a vaccinia virus genome using homologous recombination. The specific outcome is a rIBV derived from a complete cDNA copy of the IBV M41 genome.

We have subsequently modified the M41 strain of IBV to investigate the role of accessory proteins and replicase non-structural proteins in replication of IBV in vitro and pathogenicity in vivo. We have generated a panel of recombinant viruses that we can use to answer further research questions. We have assessed the use of some of these recombinant IBVs with reduced pathogenicity as vaccines that can be administered to hatched chicks or to embryos as they are developing inside the egg.
Exploitation Route Development of rationally attenuated IBV vaccines by poultry vaccine companies. The M41 cDNA has been modified to identify regions of the genome that may be deleted or modified for the generation of rationally attenuation for the development of a new generation of IBV vaccines. We have been awarded a BBSRC link grant and a BBSRC Follow on Fund grant to continue this research.
Sectors Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology

 
Description Two patents have been filed for this work and although the funding for this project by BBSRC has ended, this is being continued with industrial support. Papers are currently being produced for publication once IP restrictions have been lifted. A new BBSRC link grant and a BBSRC Follow-on Fund grant have been funded to continue this research.
First Year Of Impact 2016
Sector Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology
Impact Types Societal

 
Description Contribution to a POSTnote on 'Reducing UK Antibiotic Use in Animals'
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
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 British Egg Marketing Board PhD studentship
Amount £76,000 (GBP)
Organisation British Egg Marketing Board 
Sector Private
Country United Kingdom
Start 10/2018 
End 09/2022
 
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 10/2018 
End 03/2020
 
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  
 
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 Optimisation of preparation of TOCs from adult chickens 
Description Tracheal organ cultures (TOCs) are prepared from chicken embryos and used to assess growth of avian viruses that are not able to be propagated in cell culture. We have optimised the method of TOCs preparation from 3-week old chickens and are using these to assess viral genetic stability and phenotype in organ cultures that are a similar environment to the site of replication in whole chickens. 
Type Of Material Cell line 
Year Produced 2018 
Provided To Others? No  
Impact We hope that this technique will reduce the number of chickens required for in vivo experiments, in line with the 3Rs, and plan to publish the method in due course. 
 
Description Collaboration with University of Cambridge 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution We have performed in vitro experiments with infectious bronchitis virus, contributed to data analysis, preparation of manuscripts and discussed further funding opportunities.
Collaborator Contribution Our partners have analysed viral transcription and translation, and host gene expression after infection of host cells with infectious bronchitis virus, prepared manuscripts and discussed further funding opportunities.
Impact Dinan, A., Keep, S., Bickerton, E., Britton, P., Firth, A. and Brierley, I. (2019) Comparative analysis of gene expression in virulent and attenuated strains of infectious bronchitis virus at sub-codon resolution. J. Virol. 93(18) e00714-19.
Start Year 2012
 
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 Partnering with National Taiwan University 
Organisation National Taiwan University
Country Taiwan, Province of China 
Sector Academic/University 
PI Contribution We have prepared and submitted an application for a BBSRC-Taiwan Partnering Award to study "Assembly of Recombinant Infectious Bronchitis Virus and Determination of Antigenic Sites that Confer Hemagglutination Activity".
Collaborator Contribution The partners conceived the project and got in contact about submitting an application for funding together.
Impact An application has been made for a BBSRC-Taiwan Partnering Award in November 2018.
Start Year 2018
 
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 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 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 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 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 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 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 case study 
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 Public/other audiences
Results and Impact Case study written by the BBSRC strategy and policy officer to showcase the impact of the grant.
Year(s) Of Engagement Activity 2016
 
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