Genetic mapping of vector competence in Culicoides sonorensis

Lead Research Organisation: The Pirbright Institute
Department Name: UNLISTED

Abstract

Culicoides midges act as vectors of more than 50 arboviruses (viruses transmitted by arthropods vectors), including some of the most economically damaging diseases of livestock that are of international, economic and animal-welfare importance. These include Bluetongue virus (BTV) and African horse sickness virus (AHSV). In 2006 the first cases of BTV in Northern Europe in recorded history were detected in the Netherlands. The virus subsequently spread across a vast area of Europe, causing the most costly single outbreak of bluetongue (BT) in recorded history, with losses running into hundreds of millions of Euro's. The disease arrived in South-East England during August 2007, and only a rapid vaccination campaign prevented its re-emergence in the UK during 2008. This is estimated to have saved the UK ~£485 million. The whole of Europe must now be regarded as 'at risk' from further outbreaks of BT and other arboviral diseases including African horse sickness virus (AHSV). The latter is one of the most feared pathogens of horses with mortality rates in susceptible populations that can reach 95%.

It is already known that variation in midge genes influences their ability to become infected by BTV and to subsequently infect animal hosts (this is termed their vector competence). This has a major impact on the distribution of BTV worldwide, as the virus can only survive for long periods where competent midges are present. We aim to discover what genes control this vector competence. To do this we will first generate the complete genetic map (genome) for this group using colonies of Culicoides sonorensis held at IAH. To date, similar genomes have been produced for three mosquitoes with additional projects underway for the tsetse fly, the sandfly, the blackfly, the housefly and additional mosquito vector species. Full genome sequencing has not yet been attempted for any Culicoides species although we have generated preliminary sequencing data that shows that this can beachieved relatively rapidly with recent technological advances.

Once we have produced the genetic map of the midge we will then examine and catalogue all genetic differences between the individual midges in the population. This information will allow us to identify different versions of genes that influence the ability of the midge to become infected and transmit viruses (specifically BTV and AHSV). In addition to providing knowledge of how Culicoides and these viruses interact, our proposal will also generate the first annotated genome for this insect vector group. This will provide vast new opportunities in research on these important disease vectors. It will also allow us to compare the genes from C. sonorensis with other insect groups (e.g. mosquitoes) for which genome sequences are already available. The genome sequence of Culicoides generated in this study will also provide a long term fundamental tool for understanding the reasons which both BTV and AHSV are restricted in distribution and also why incursions such as that of BTV into northern Europe occur.

Technical Summary

Culicoides biting midges inflict substantial economic damage on global livestock production and trade by acting as vectors of arboviral pathogens such as bluetongue virus (BTV). The hypothesis this proposal addresses is that genetic variation within species influences the vector competence of Culicoides for BTV strains and hence impacts upon the epidemiology of this virus worldwide. One of the fundamental steps in the genomic approach to understanding complex traits, such as vector competence, is the correlation of phenotypic data with genotypes in order to identify quantitative trait loci (QTL). Here we propose a genome-wide association study (GWAS) to identify the underlying genes that control vector competence in the insectary reared Culicoides sonorensis colonies. Toward this aim, we will generate the first annotated genome sequence of any Culicoides biting midge and identify genome-wide SNP markers for genetic mapping of vector competence traits.

To fulfil the objectives outlined in this proposal we will use the unique IAH C. sonorensis colonies and cell lines to:
1. Produce an annotated genome sequence for Culicoides sonorensis
2. Generate a catalogue of genetic diversity for Culicoides sonorensis
3. Develop a C. sonorensis SNP panel for vector competence GWAS
4. Perform an association analysis of vector competence traits in C.sonorensis
The primary outcome of this project will be the elucidation of the genetic basis of vector competence of C. sonorensis for bluetongue and African horse sickness viruses. This will provide fundamental insights into arbovirus: Culicoides systems that to date remain poorly characterised. It will also generate the first accurately annotated genome of a Culicoides species worldwide opening up vast opportunities for comparative genomics. The genome sequence will underpin advances in improving food security by protecting UK agriculture from potentially catastrophic exotic animal diseases.

Planned Impact

The primary deliverable of this project will be the elucidation of the genetic basis of vector competence of C. sonorensis for bluetongue virus (BTV) and African horse sickness virus (AHSV). It will also generate the first accurately annotated genome of a Culicoides species worldwide. There is significant potential for this research to facilitate the development of new control strategies for these important animal diseases, with consequences for agricultural practice and food security, both in the UK and worldwide.

While the primary focus of the project will be academic, a range of different groups will additionally benefit from the results, and we have formulated plans to engage them in the project. Worldwide, EU and UK policy makers in Animal Health will have an interest in the results due to their relevance to the geographic distribution of BTV and AHSV, and will be engaged through SC and PM's roles in OIE (World Animal Health) expert groups on Culicoides and BTV in Defra's BTV experts group. The Animal Health Industry benefits through the production of a Culicoides genome allowing development of long-term control techniques. They will be engaged through contacts both with major companies already pursued by MF, SC, PM and PK but also through a meeting on Genomics in Animal Health held in year three of the project by the society for chemical industry.
Outreach activities will be conducted to ensure that Farmers and Veterinarians benefit from the project, by gaining a deeper understanding of Culicoides and the pathogens they transmit. The high profile nature of the incursion of recent BTV-8 incursions has facilitated an opportunity to provide background information to farmers and veterinarians on what was until recently viewed as exotic pathogens of little relevance to the UK. We intend to build on this advance by publishing at least three trade articles each year across veterinary and farming publishing, detailing significant findings made during the project and how we intend to turn research into practice.
Finally, we will engage with the General Public who will have an interest in both the advanced nature of the techniques involved in the study and the high profile of Culicoides as a vector group in the UK. We will exploit this unique opportunity initially through the provision of press releases to media outlets at the initiation of the project, to both promote the objectives of BBSRC and explore this area of science in an understandable fashion. Scientists employed during the project will also be encouraged to take part in public engagement. In addition, the entomology group has wide experience of outreach activities through a variety of events run primarily with the Royal Entomological Society and these will also be utilised for this project. We additionally, however, propose to attend and run an exhibit at "Pestival", the largest entomological outreach festival worldwide. Funds are requested to allow travel for four staff (MF, SC and IAH workers) to attend this activity. Exhibit materials will also be used in further outreach and in open days for IAH, TGAC and EBI. Finally, our laboratory is already involved in STEM (Science, Technology, Engineering and Mathematics) activities for schools. 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. All researchers will be encouraged to participate in STEM activities including school visits.
Throughout the project we will utilise e-outreach by providing a description and updates of the project for a general audience through institute websites (IAH, TGAC and EBI). IAH will also produce in association with the BBSRC press office, two videos describing our work for a general audience that will be released during year one (a basic introduction to the group and the project) and year three (the results of the project and future utility).
 
Title Culicoides animations 
Description This project was funded by a BBSRC responsive mode grant and was initiated on 1st February 2013. Culicoides biting midges inflict substantial economic damage on global livestock production and trade by acting as vectors of arboviral pathogens. The hypothesis that our project addresses is that genetic variation within species influences the vector competence of Culicoides for BTV strains and hence impacts upon the epidemiology of this virus worldwide. The primary deliverable of this project is the elucidation of the genetic basis of vector competence of C. sonorensis for bluetongue virus (BTV). It will also generate the first accurately annotated genome of a Culicoides species worldwide opening up vast opportunities for comparative genomics. This will provide fundamental insights into arbovirus: Culicoides systems that to date remain poorly characterised. The genome sequence will underpin advances in improving food security by protecting UK agriculture from potentially catastrophic exotic animal diseases. There is significant potential for this research to facilitate the development of new control strategies for these important animal diseases, with consequences for agricultural practice and food security, both in the UK and worldwide. While the primary focus of the project is academic, a range of different groups will additionally benefit from the results, and we have formulated plans to engage them in the project. One of the principal approaches for the dissemination of the outputs for this project has been the production of animated videos funded by the "Excellence with Impact" competition. This novel approach of using animations to describe our work to a general audience goes above and beyond the intended scientific audience of the project. This has also been of interest to the Animal Health Industry who will benefit through the production by engaging with the public. The animations have also been used in outreach activities to ensure that Farmers and Veterinarians benefit from the project, by gaining a deeper understanding of Culicoides and the pathogens they transmit. The high profile nature of the incursion of recent BTV-8 incursions has facilitated an opportunity to provide background information to farmers and veterinarians on what was until recently viewed as exotic pathogens of little relevance to the UK. We intend to build on this advance by further engagement across the veterinary and farming stakeholders, by detailing significant findings made during the project and how we intend to turn research into practice. Finally, we will engage with the Schools who will have an interest in both the advanced nature of the techniques involved in the study (STEM) and the high profile of Culicoides as an insect vector group in the UK. We will exploit this unique opportunity through the animated videos to both promote the objectives of BBSRC and explore this area of science in an understandable fashion. Scientists employed during the project are encouraged to take part in public engagement. In addition, the entomology group has wide experience of outreach activities through a variety of events run primarily with the Royal Entomological Society and the animated videos will also be utilised for this engagement. Exhibit materials, including the animated videos, will be used in further outreach and in open days for The Pirbright Institute, TGAC and EBI. Finally, our laboratory is already involved in STEM (Science, Technology, Engineering and Mathematics) activities for schools. 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. All researchers will be encouraged to participate in STEM activities including school visits and career days. 
Type Of Art Film/Video/Animation 
Year Produced 2015 
Impact This has been selected for the final of the BBSRC Excellence with Impact awards. 
 
Description This project is progressing well. Many collaborative projects have resulted from this work. Final publication of this work completed.
Exploitation Route The imminent public release of the Culicoides genome is of enormous significance to researchers of vector borne diseases.
Sectors Agriculture, Food and Drink,Environment,Healthcare

URL http://www.pirbright.ac.uk/research/GeneticsGenomics/Default.aspx
 
Description This grant is ongoing and has sucessfully produced the first ever genome sequence of the diseae insect vector of the Culicoides genus. While the primary focus of the project is academic, a range of different groups will additionally benefit from the results, and we have formulated plans to engage them in the project. One of the principal approaches for the dissemination of the outputs for this project has been the production of animated videos funded by the "Excellence with Impact" competition. This novel approach of using animations to describe our work to a general audience goes above and beyond the intended scientific audience of the project. This has also been of interest to the Animal Health Industry who will benefit through the production by engaging with the public. The animations have also been used in outreach activities to ensure that Farmers and Veterinarians benefit from the project, by gaining a deeper understanding of Culicoides and the pathogens they transmit. The high profile nature of the incursion of recent BTV-8 incursions has facilitated an opportunity to provide background information to farmers and veterinarians on what was until recently viewed as exotic pathogens of little relevance to the UK. We intend to build on this advance by further engagement across the veterinary and farming stakeholders, by detailing significant findings made during the project and how we intend to turn research into practice. Finally, we will engage with the Schools who will have an interest in both the advanced nature of the techniques involved in the study (STEM) and the high profile of Culicoides as an insect vector group in the UK. We will exploit this unique opportunity through the animated videos to both promote the objectives of BBSRC and explore this area of science in an understandable fashion. Scientists employed during the project are encouraged to take part in public engagement. In addition, the entomology group has wide experience of outreach activities through a variety of events run primarily with the Royal Entomological Society and the animated videos will also be utilised for this engagement. Exhibit materials, including the animated videos, will be used in further outreach and in open days for The Pirbright Institute, TGAC and EBI. Finally, our laboratory is already involved in STEM (Science, Technology, Engineering and Mathematics) activities for schools. 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. All researchers will be encouraged to participate in STEM activities including school visits and career days.
Sector Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic

 
Description Contributed to Chief Medical Officers report- Genomics section
Geographic Reach Europe 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
URL https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/6310...
 
Title Culicoides genome sequence 
Description The preliminary data for the Culicoides genome sequencing is already proving to be of great interest to a number of groups and people, both within the Institute and beyond. 
Type Of Material Technology assay or reagent 
Year Produced 2014 
Provided To Others? Yes  
Impact The preliminary data for the Culicoides genome sequencing is already proving to be of great interest to a number of groups and people, both within the Institute and beyond. 
 
Description EBI Culicoides genome project 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Performed experiments and provided material for Sequencing and genome build of the Culicoides genome project
Collaborator Contribution Sequencing and genome build for Culicoides genome project.
Impact Publication and public release of genome data for Culicoides genome project
Start Year 2013
 
Description Genetic mapping of vector competence in Culicoides sonorensis. 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution The primary deliverable of this project will be the elucidation of the genetic basis of vector competence of C. sonorensis for bluetongue virus (BTV) and African horse sickness virus (AHSV). It will also generate the first accurately annotated genome of a Culicoides species worldwide.
Start Year 2012
 
Description USDA Culicoides 
Organisation U.S. Department of Agriculture USDA
Department National Animal Disease Center
Country United States 
Sector Public 
PI Contribution Combined data for Culicoides genome project to enable publication in high impact journal.
Collaborator Contribution Transcriptomics data for vector competence analysis and genome build.
Impact Combined data for Culicoides genome project to enable publication in high impact journal.
Start Year 2014
 
Description Chair of organising Committee for Wellcome Trust-Animal Genetics and Diseases 2017 
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 This meeting brought together specialists working on the interface between genomics, genetic engineering and infectious disease with the aims of improving animal and human health and welfare.

Scientific sessions included:
Genetics of immune responses and disease resistance
Genetically engineered livestock (including genome editing)
Quantitative genetics and epigenetics applied to disease
Epidemiology and pathogen evolution
Bioinformatics, comparative and functional genomics
Precision medicine of animal companions
Year(s) Of Engagement Activity 2017
URL https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=635&dm_i=2SUU,HOGH,4R4AW1,...
 
Description Holt School Surrey. Bee meadow & A-level outreach Talk. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I discussed the importance of pollinators for biodiversity and food security with the younger students. I also discussed careers in science with A-Level students. There was good interaction and many questions surrounding both topics.
Year(s) Of Engagement Activity 2018
 
Description Innovate Guildford Outreach (12th March) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact With amazing exhibits, activities, workshops, talks and competitions, it's FREE to attend. Explore the four zones: Engineering, One Health, Digital Media and Future Living, experience interactive performances, hear inspiring speakers (including leading gaming pioneer Peter Molyneux and animal health pioneer Professor Nick Bacon) and take in an amazing atmosphere. Theatre, music and comedy will feature through the day, with everything from how technology might have affected Shakespeare's plays to risky recycling and photographic secrets.
Year(s) Of Engagement Activity 2017
URL https://www.guildford.gov.uk/innovateguildford
 
Description Kingdown School Warminster Wiltshire talk to 6th form students about career in science. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I presented my career path to the students to engage them on STEM careers. I had a good level of discussion and many questions.
Year(s) Of Engagement Activity 2018
 
Description MF PAG 
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 The Plant and Animal Genome XXIV Conference (PAG) is designed to provide a forum on recent developments and future plans for plant and animal genome projects. Consisting of technical presentations, poster sessions, exhibits and workshops, the conference is an excellent opportunity to exchange ideas and applications on this internationally important project.
Year(s) Of Engagement Activity 2014,2016
 
Description STEM Outreach Event (Farnborough, 9th November) 
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 Public/other audiences
Results and Impact See web link
Year(s) Of Engagement Activity 2016
 
Description Winston Churchill Careers Fair. Winston Churchill School, Hermitage Road, St Johns, Woking, Surrey, GU21 8TL 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact AS attended and presented at this event to stimulate increased interest in science and research.
Year(s) Of Engagement Activity 2018