Restriction of avian viruses by host interferon-inducible transmembrane proteins (IFITMs).

Poultry products are the main source of animal protein for human consumption worldwide. Current global production is 55 billion chickens per year. Global population growth and rising affluence are fuelling demand for poultry meat and eggs, and a need exists to increase their supply. The UK poultry industry contributes around £3.4bn to the UK economy. Viruses that infect poultry create major challenges to animal health through loss of productivity and disease. These have simultaneous effects on the global poultry industry through a reduction in the output of poultry meat and eggs. Birds often carry viruses in the absence of any clinical symptoms; however some types of viruses cause severe diseases in poultry that exert substantial animal welfare and economic costs. Therefore, developing efficient control strategies against these viral diseases is crucial for the poultry industry, but also very important in alleviating poverty in developing countries, where these diseases are widespread, causing devastating effects on poultry farming.

Recent evidence has revealed that a family of proteins produced in human cells is able to limit the entry processes and replication of several very dangerous human viruses. Direct clinical relevance of the involvement of these proteins in viral diseases has recently been shown in patients hospitalized with the seasonal flu viruses. In this study researchers showed that more patients with severe symptoms had a particular version of the protein that is not commonly found in the population. These results reveal that the action of these proteins can profoundly alter the course of flu infections by limiting the spread of virus in the body's cells. Although these proteins have been well characterised in human and mouse, little data exists for other species. To date only limited details of two such proteins have been published in chickens; thought to be equivalent to two of the five known human proteins. No characterisation has been undertaken of the role that these chicken proteins play in the control of avian viruses. Since these proteins appear to be the first line of defence against infection, this suggests that individual chickens or entire poultry flocks with more active versions of the protein may be more resistant to avian influenza virus and other pathogenic poultry viral diseases. The research set out in this proposal will play a fundamental part in explaining how both the gene and protein are linked to viral susceptibility in chickens. Our preliminary work leading to this proposal has established that chickens do indeed have similar version of these proteins, and that they can protect against influenza infection.

It is highly plausible that variation affecting these proteins, as is seen in the human population, explains why some birds are more susceptible to viral infections. By analysing the genetic material of birds that differ in levels of resistance to these viruses, we hope to identify the chicken versions of these proteins that give protection, both in laboratory and commercial chickens. Analysis of these proteins in the chicken presents opportunities not just for a greater understanding of increased viral resistance, but also as tools to combat viruses in the poultry industry. It may be feasible to selectively breed for birds with improved resilience to viral infections; however this requires the identification of resistance-associated factors and knowledge of how they act.

The aim of this proposal is therefore to understand the biology and any genetic changes of these genes in chickens. Specifically we will examine the ability of the genes to protect the chickens against viruses. The output of this project will be in identifying versions of these proteins that give resistance to a number of avian viruses. Poultry breeding companies will then be able to select the protective version of the genes encoding these proteins in all future breeding programmes.

Recent evidence has revealed that a family of interferon-inducible transmembrane (IFITM) proteins restrict the entry processes and replication of several highly pathogenic human viruses. We have now established that chickens encode functional IFITM3 orthologues that restrict influenza infection in vitro. We hypothesise that certain chIFITM allelic variants confer reduced or enhanced levels of protection to endemic and emerging viruses such as Infectious Bronchitis Virus (IBV), Infectious Bursal Disease Virus (IBDV) and avian influenza virus (AIV). IFITM proteins represent clear opportunities, not just for a greater understanding of enhanced viral resistance, but also as tools to combat these pathogenic viruses in the poultry industry, including viruses with zoonotic potential.

To address the objectives we have set out in this proposal we will answer three main questions:

1. Do chIFITMs restrict diverse avian viral pathogens?
This will define the breadth of antiviral activity of the chicken IFITM locus to important avian pathogens and the consequence on other antiviral genes of altering chIFITM expression levels.

2. What is the level of expression and genetic variation at the IFITM locus within inbred, commercial and outbred broiler and layer breeds?
This analysis will establish within and between breed diversity, and identify rare, potentially protective variants. It should also indicate if selection for production traits in the commercial lines has compromised population susceptibility to avian viral diseases. These markers will also prove useful for any future association analysis at the IFITM locus.

3. To what extent do individual alleles of IFITM genes confer resistance to IAV, IBD and IBDV?
This will characterise the in vivo significance of different chIFITM alleles and provide defined polymorphisms as breeding markers to improve intrinsic resistance to important avian virus pathogens.

With current global production of 55 billion chickens annually, poultry products are the main source of animal protein for human consumption worldwide. The sustainability of this major food resource is now a global research priority. The UK poultry industry currently contributes around £3.4bn to the economy. Avian viruses, such as avian influenza, Infectious Bursal Disease Virus and Infectious Bronchitis Virus create major challenges to poultry health through loss of productivity and mortality, and have concomitant effects on the global poultry industry through a reduction in the output of poultry meat and eggs. Developing efficient control strategies against these viral diseases will not only of benefit Western societies, but also alleviate poverty in developing countries, where these diseases are widespread, causing devastating effects on poultry farming.

The primary focus of this study will be the academic work necessary to underpin and facilitate a range of benefits for different stakeholders. The discovery of the role of IFITM proteins as broad spectrum, anti-viral agents for avian viruses will provide new insights into innate immunity and potentially novel tools and breading programs with which to counter viral pathogens of poultry. The work will create opportunities for medium term industrial outcomes from this project, and we will formulate plans to engage industry in the project. One of the main beneficiaries of this work will be the livestock industry, and specifically poultry breeding companies. Two of the world leading companies, Aviagen and Cobb-Vantress are partners in this Animal Health Research club and thus results generated by this project has a great potential to benefit their global economic performance, and specifically the economic competitiveness of the UK poultry industry. Worldwide, it is likely that the EU and UK policy makers in Animal Health will have an interest in the results due to the impact that the poultry industry has on food sustainability. Outreach activities will be conducted to ensure that stakeholders benefit directly from the project, by gaining a deeper understanding how we intend to turn this research into practice.

We will have impact on the professional development of the scientists involved in this work. In addition to laboratory- and animal-based training, the staff employed on this project will have access to training courses on scientific methods, technical writing, presentation skills, ethics, and transferable skills courses provided by the Pirbright Institute and WTSI. They will also train new staff members and visitors to perpetuate skills and benefit from working with leading poultry companies during the project. Throughout the project we will utilise e-outreach by providing a description and updates of the project for a lay public through the Pirbright Institute and Sanger websites. IAH will also produce a video describing our work for a general audience that will be released during year one (a basic introduction to the project) and year three (the results of the project and future utility). We will engage with the General Public through the provision of press releases to media outlets at the initiation of the project; to both promote the objectives of BBSRC's Animal Health Research Club, and to explore this area of science in an understandable fashion. Scientists employed during the project will also be encouraged to take part in public engagement. Dr Fife is an active STEM ambassador, which creates opportunities to inspire young people and develop their creativity, problem-solving and employability skills the UK's future competitiveness. Prof Kellam gives science presentations to junior and secondary school children and all researchers will be encouraged to participate in STEM activities including school visits.