Towards control of Infectious bronchitis virus; understanding cross protection and genetic plasticity of IBV

Lead Research Organisation: The Pirbright Institute
Department Name: Coronaviruses

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. Infectious bronchitis virus (IBV) is an endemic virus that causes severe disease outbreaks in chickens worldwide; it affects the global production of meat-type birds, due to problems in weight gain and quality, and egg production through decreasing the numbers and quality of eggs produced. Effective and economically viable vaccines against IBV are available, but multiple combinations of available vaccines are needed because the level of cross-protection against different IBV strains is insufficient. Poor cross-protection is the result of variation in a major surface protein of the virus (the spike (S) protein). New variant strains of IBV with differences in the S protein appear regularly in the field and, through analysis based on the sequence of the S protein, it is impossible to predict which vaccines will induce protection against the newly emerged viruses. Only elaborate and expensive testing in chickens elucidates which vaccine combination is needed to protect against a new strain of IBV.

This proposal will address the seemingly unpredictable nature of the virus. The availability of a unique reverse genetics system for IBV has the potential to lead to the development of a new generation of live vaccines. In this proposal we will generate recombinant viruses that are identical, except for the immunodominant S1 subunit, of the economically most important IBV strains (M41, 4/91 and QX). Vaccination-challenge experiments with the same and with different viruses will identify if there are different degrees of protection. The causes of insufficient and unpredictable levels of cross-protection are the main focus of this study. Ultimately we will determine the key regions or epitopes on the S1 subunit of the economically most important IBV strains that are responsible for inducing protective immune responses. We will use novel "epitope fingerprinting" technology to determine the key regions (epitopes) that are recognised by the antibodies induced after vaccination. Identification of key regions following vaccination with a single IBV strain or multiple strains will allow us to determine which epitopes are needed by a vaccine to induce protection. When new virus strains emerge we will then be able to predict which vaccines will be required to induce effective protection against the new virus strain.

Moreover, we will further develop our understanding of how pressure from the bird's immune responses on the virus might drive the virus to change or mutate. This will involve the passage of an IBV strain in eggs, in the same way as vaccines are produced. However, the replication of the virus will be put under immune pressure by the addition of antibodies specific for this virus. This will essentially mimic the immune pressure applied to the replicating virus, as occurs naturally after vaccination but without testing this in birds. Using contemporary deep sequencing technology we will identify the molecular changes that occur as a result of immune pressure and the process by which the virus is able to evade the applied vaccine, potentially evolving into a new variant. By understanding and manipulating the processes that govern virus adaptation after vaccination, we aim to identify ways of reducing the danger of vaccine strains changing and causing damaging disease outbreaks.
Results from this proposal will provide (1) crucial information on why vaccines used to control an important avian endemic pathogen IBV fail to induce cross-protection, (2) information for the efficient use of existing vaccines and (3) the development of more efficient vaccines, thus ensuring that poultry farming remains not only a secure food source but also increases the economic competitiveness of the UK.

Technical Summary

The overall aim of this project is to address the unresolved question "which epitopes can induce cross-protection between infectious bronchitis virus (IBV) strains and are these epitopes prone to mutate under immune pressure?"
We will generate isogenic recombinant viruses (rIBV) expressing the immunodominant part, S1, of the S protein of the economically important IBV strains, M41, 4/91 and QX. Using in vivo vaccination-challenge experiments we will assess (i) whether homologous S1 can induce full protection, (ii) whether vaccination with heterologous S1 can induce cross-protection and (iii) if maternally derived antibodies affect the induction of protective immune responses. As the rIBVs are isogenic, any immune responses against other IBV proteins will be similar between birds. Birds will be sampled during the course of the infections to analyse the tropism of rIBV and local cellular infiltrates by immunohistology. These studies will provide a unique set of S1-specific antibodies that are induced against the different S1 sequences. These sera will be used to define the immunogenic epitopes on S1 of the 3 viruses. The epitopes will be assessed by CLIPS technology, using peptides that are fixed into defined three-dimensional structures resulting in functional mimics of complex binding sites. The epitope mapping data will determine whether the epitopes are closely located, overlapping within the S1 sequences or if they are independent and specific to the serotypes. Knowledge about the protective epitopes will be used to investigate the predictive value of S1 sequences of other IBV serotypes for protection. Finally we will test the genetic plasticity of rIBV and determine the pattern and frequency of viral polymorphisms during egg passage under immune pressure with polyclonal chicken sera and monoclonal antibodies specific for defined epitopes on S1. Newly emerged viruses will be deep sequenced and we will determine if antigenic shifts result in a shift in serotype.

Planned Impact

Viral diseases are a constant threat to the poultry industry through reduction in broiler production, decreases in egg production & quality, and effects on animal welfare. IBV causes an acute highly contagious and economically important respiratory disease causing economic losses to the global poultry industry. Beyond the academic scientific community, the proposed research may also realise tangible benefits of a social and economic nature. These will be of benefit to The RI and TPI, the BBSRC and its stakeholders. The outcomes of the research will be of interest to other groups such as the Poultry industry, vaccine producers, DEFRA, veterinarians, students and the general public. Engagement with these diverse groups will be achieved via meetings, articles in the trade press, tailored webpages and press releases to the media. Overall the proposed research will have the following impacts:-

UK economy: A 2005 DEFRA-funded report estimated that IBV affects 22 million birds in the UK, incurring and overall cost of £23 million per annum. 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. It has been estimated that every 10% reduction in IBV would be worth around £2.4 million to the UK Industry and £654 million globally. Infectious bronchitis was ranked by the commercial sector as the second most important disease of poultry in terms of the number of affected poultry between 2006 and 2009 and accounted for the largest segment (24.3%) of the poultry diseases market in 2012; this is expected to increase by 7.8% from 2013-2018.

BBSRC: Food security is a key research priority in the BBSRC Strategic Plan. Results from this project will provide crucial information as to why vaccines used to control an important avian endemic hogen fail to induce cross-protection, on the use of existing vaccines and on the development of 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 to the global poultry industry. In 2012 the UK poultry meat industry sales were £6.1 billion; £3.3 billion contributed to UK GDP, with every £1 billion generating another £1.3 billion in the rest of the UK economy and supporting 73,200 jobs. Improved efficiency of the industry, through improved protection against endemic diseases such as IBV and the development of more efficient vaccines, particularly against continually emerging variants, will have positive benefits both socially and for the UK economy. Unravelling the mechanisms of cross protection will allow us to predict the combinations of vaccines needed to protect against multiple strains in the field, improving animal welfare, reducing losses to the poultry industry and risks to food security.

Pharmaceutical companies: Both groups (RI and TPI) have established collaborations, including direct support, with several vaccine companies that have resulted in ongoing assessment of potential vaccine candidates and immunomodulatory products. The data generated during this project will allow us to predict which combinations of the currently available vaccines are needed in the field to protect against current and newly emerging IBV strains.

Academia and Training: Results with respect to mechanisms of cross-protection, epitope prediction and the effect of immune pressure on virus mutation will be of interest to a wide scientific community and will be published in peer-reviewed journals and presented at national and international scientific meetings. The project will provide training in immunology, epitope mapping, molecular virology and bioinformatics.

Publications

10 25 50
 
Description We have evaluated the protection induced by recombinant infectious bronchitis viruses (rIBVs) against virulent challenge in chickens. We found that viruses expressing whole spike glycoproteins were better able to protect against a homologous challenge strain than viruses expressing either the S1 or S2 subunit of the homologous challenge strain. This may be due to conformational changes in the chimaeric spike glycoproteins, or protective epitopes may be required across both subunits for stimulation of an optimal immune response.

In a subsequent vaccine efficacy experiment in chickens, we evaluated the protection offered by rIBVs expressing different spike glycoproteins against challenge with a heterologous strain. Chickens were not fully protected and we are continuing to investigate this. Extending the replication time of the vaccine candidates in chickens or altering the composition of the structural proteins from the challenge strain expressed in the vaccine strain may improve levels of protection.
Exploitation Route These findings will be used to inform further research questions and the rational design of next generation vaccines to protect against infectious bronchitis virus.
Sectors Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology

 
Description Results of this research have been presented at national and international conferences, facilitating networking and discussion of future collaborations. We have discussed the findings with contacts in the poultry industry.
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 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. 
 
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
 
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 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 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
 
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 Presentation at BBSRC ARC meetings 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation of research at BBSRC Animal Health Research Club meetings. Members from industry and other academic institutes present. Discussion of results followed.
Year(s) Of Engagement Activity 2015,2016,2017
 
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 and 2019. I discussed my work and future collaborations with other virology researchers working in the UK.
Year(s) Of Engagement Activity 2016,2017,2018,2019
 
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
 
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