Genetic mapping of vector competence in Culicoides sonorensis.

Lead Research Organisation: EMBL - European Bioinformatics Institute
Department Name: Ensembl Genomes


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 be achieved 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).


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Description We have assembled and annotated the first complete genome sequence of a Culicoides midge. Comparative analysis has established the differences in the genome between the midge and other related species. The annotation has been used to identify candidate genes with a role in vector competence (for transmission of viral pathogens of critical importance to agriculture).
Exploitation Route Our findings have been published in the peer-reviewed literature. The sequence and annotation have been made accessible to the community via the website of the European Nucleotide Archive for use by researchers working on midge-transmitted diseases; and will be additionally made available through the Ensembl Metazoa website ( shortly.
Sectors Agriculture, Food and Drink,Chemicals,Pharmaceuticals and Medical Biotechnology

Description The project has generated reference genome sequence, annotation and transcriptome data from Culicoides sonorensis, now described in the peer-reviewed scientific literature. The data has been released to collaborators, and to the scientific public (via the European Nucleotide archive) and has been used by groups studying the vector competence for transmission of viral parasites, information of importance in the design of control strategies.
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

Amount £66,863 (GBP)
Funding ID BB/M028372/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2015 
End 10/2018
Title Culicoides genome database 
Description A database providing public access to the Culiocides genome and annotation developed in the project, made available to the scientific community via an interactive toolset (including genome browser) and choice of API. The database is integrated within the Ensembl Metazoa framework providing comparative analysis against other metazoan species. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact The Culiocides genome can be browsed and compared against other invertebrate genomes.