ANIHWA call2: Can we predict emergence and spread of Culicoides-borne arboviruses in Europe according to genetic drivers

Lead Research Organisation: The Pirbright Institute
Department Name: Entomology

Abstract

Culicoides biting midges (Diptera: Ceratopogonidae) are currently the most important biological vectors of livestock arboviruses in Europe. Outbreaks of bluetongue virus (BTV) and Schmallenberg virus (SBV) continue to have a significant economic impact through clinical disease and the imposition of animal trade movement restrictions. At least three Culicoides-borne viruses recently identified in Europe possess an unknown origin, hence future outbreaks involving described or undescribed strains or species of Culicoides-borne viruses have a high potential of occurring in the future. These viruses could include further incursions of known arboviruses (including additional species of Culicoides-borne
arboviruses such as African horse sickness or Epizootic Haemorhagic Disease Virus) or as yet undescribed species with an unknown pathogenicity to livestock or humans.

In this project we will dissect Culicoides vector-arbovirus relationships across multiple ecosystems and species and in unprecedented detail to provide data useful for both defining risk of incursion and subsequent spread. Using newly developed methods to blood-feed Culicoides viruses of epidemiological interest, we will assess barriers associated with vector competence that may underlie restrictions to arbovirus movement in Europe. The fundamental genetic drivers determining vector competence in Culicoides will then be explored using genomic techniques to identify panels of candidate genes influencing this process. Following identification, comparative genomics will identify species specific differences in panels which will be examined across ecosystems in Northern and Southern Europe. In addition, we will also examine the virome of European
Culicoides of veterinary importance as a potential influence on vector competence and as a means of understanding how viral diversity within populations can be used to infer risk of outbreak. Using metagenomic analyses we will examine viromes from Culicoides populations across the participating countries that have already been the subject of targeted sampling for surveillance purposes. We expect this to reveal for the first time the true diversity of viruses present within Culicoides and to begin to untangle their role in the epidemiology of pathogenic virus transmission, opening a new field of research for animal virus vectors.

Technical Summary

Culicoides biting midges (Diptera: Ceratopogonidae) are currently the most important biological vectors of livestock arboviruses in Europe. Outbreaks of bluetongue virus (BTV) and Schmallenberg virus (SBV) continue to have a significant economic impact through clinical disease and the imposition of animal trade movement restrictions. At least three Culicoides-borne viruses recently identified in Europe possess an unknown origin, hence future outbreaks involving described or undescribed strains or species of Culicoides-borne viruses have a high potential of occurring in the future.

While the impact on animal health of these outbreaks has been geographically broad, this masks a complex and incomplete epidemiological picture characterized by differential spread in Europe of arbovirus strains. In the Mediterranean basin, studies by Partners 3 and 4 have demonstrated that transmission of arboviruses is dominated by C. imicola, an afrotropical species that is highly abundant in this region. In contrast, Partner 1 has shown that transmission in Northern Europe is dominated by a range of vectors of which the most convincingly implicated is the C. obsoletus/C. scoticus complex. To date, standardized comparison of vector competence for arbovirus strains between these vector groups have not been conducted with studies limited to single countries. This currently prevents examination of barriers to movement of arboviruses between Southern and Northern Culicoides-arbovirus 'episystems'. Following the recent initiation of the Culicoides genome project (Partners 1 and 2: BBSRC project BB/J016721/1) and advances in technologies to dissect vector-arbovirus relationships, a unique opportunity exists to examine this area in multiple ecosystems and in unprecedented detail.

Planned Impact

The impact of CuliOme will fall on the following major areas in addition to Academic Beneficiaries outlined previously.

To key policy makers:
Contact with policy makers will be ensured by the contacts held both within the group and through direct attendance of CuliOme members in policymaking initiatives. In this regard the attendance of two CuliOme members (TPI: SC and IZS: MG) on the OIE working group for Culicoides and in EFSA working groups on BTV and SBV, will provide a natural outlet for novel discoveries. Periodic reports will be made available to ANIWHA funders upon demand, as to other stakeholders (EU, FAO, OIE, national organisations, livestock industry, policy makers). We expect the project to influence policy with regard to assessing the potential for BTV emergence in epidemic areas and additionally assessing the impact of coninfection on transmission in the field. Both of these areas should enhance the preparedness of Europe for emergence of BTV.

To the general public:
Partner 1 and 3 participate actively in communicating to the general audience on Culicoides-borne diseases related topics through websites www.bluetongue.cirad.fr and www.Culicoides.NET. Highlights of the annual reports will be released to the public via these websites. All press releases will be produced with multiple language options, taking advantage of the multi-national nature of the collaboration. Vector-borne diseases in general have a high profile both in terms of applied and fundamental interest in the public domain and we expect this project to improve understanding at a basic level. This will be achieved through measures discussed in the impact plan.

Intellectual property:
Knowledge generated by CuliOme will be defined prior to the project initiation through the drawing up of a common Memorandum of Understanding or Consortium Agreement, generated by TPI as coordinator, and being circulated to all partners following confirmation of funding. It will detail, amongst other things, IPR management relating to foreground/results, rules for dissemination and communication, task allocations, deliverables and resources for each partner, and rules governing exploitation of the results. As a general rule, intellectual property will remain the property of the specific partners involved in its development.
 
Description Within WP1, we have carried out a training exercise between IZS and Pirbright, distributed viruses as planned for parallel assessment of vector competence and fed and incubated several thousand Culicoides biting midges on these viruses using our standard artificial feeding techniques. We have then carried out standardised assays to define susceptibility to infection and compared the rates of fully disseminated infections according to country, virus strain and species of midge. These studies are expected to yield two publications in 2019, one led by Pirbright and the other by IZS, which will summarise differences in vector competence between populations and these were discussed at the annual meeting in early 2018, held at IZS. In summary, significant differences were found in infection rates between southern and northern European biting midges that may in part explain differential spread of emerging viruses in these regions.

Within WP2, representative samples of Culicoides susceptible or refractory to infection with bluetongue virus from WP1 have been collated at Pirbright. In the next few weeks, DNA will be extracted from these samples and sent for transcriptome sequencing at the Centre for Genomic Research at Liverpool, UK. These will be analysed across location, species, virus and population using gene expression analysis pipelines developed by EBI and the results collated for a single publication in 2019. It is expected that the experimental studies are completed by the project end date for Pirbright and EBI (31st January 2019). One change within this aim is that we have concentrated the studies on bluetongue virus in order to provide additional replicates for transcriptomic analysis. This was decided on the basis of an experiment that was ongoing at the point of application for this call that revealed greater individual diversity in response to infection than was originally envisaged.

Within WP3, significant progress has been made in validating metagenomics protocols for analysis of Culicoides viromes. In addition, large scale and intensive field collections have been made of approximately 80 000 Culicoides in the UK, France and Italy that have been sorted to species and centralised at Cirad in preparation for analysis. Progress on WP3 has since been interrupted by a period of maternity leave from the project postdoc at Cirad and a request for a project extension has been made (to 31/12/2019). This time will be used to screen across Culicoides populations using the validated techniques and will include IZS to complete shared milestones.
Exploitation Route Within the project there is substantial development of techniques and additionally generation of datasets that will be of interest to the wider vector-borne disease community. Within WP1 we have refined techniques for blood-feeding and analyzing infection of Culicoides biting midges which will strengthen future studies in this area. This includes standardizing the detection of arboviruses within biting midges in order to determine the level of arbovirus dissemination which is vital in demonstrating vector competence. In addition, the project will generate a series of transcriptomic datasets based on these studies which will be of use to both workers in this direct field and as a comparative resource for those working on mosquitoes, sandflies and blackflies. These will be released into the public domain as datasets. Finally, the project pioneers the use of emerging techniques in viral genomics with small biting flies which will have a significant impact on the studies of biting midges, sandflies, blackflies and other small fly pest species.
Sectors Agriculture, Food and Drink,Environment,Healthcare

 
Description International Congress of Entomology (Florida) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Chaired session and gave presentation on progress in Culicoides research. Largest ever meeting involving the Culicoides community with 100+ attendees.
Year(s) Of Engagement Activity 2016
URL http://ice2016orlando.org/
 
Description Invited Chair at European Congress of Entomology (Naples,July) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Chaired session on vector-borne diseases at meeting and subsequent question sessions with 15 minute presentation on Culicoides biting midges.
Year(s) Of Engagement Activity 2018
URL http://www.ece2018.com/scientific-programme/day-1-monday-2-july/
 
Description Lecture given to University of Surrey MSc Veterinary Microbiology students 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact A 2-hour teaching lecture given to 10 MSc Veterinary Microbiology students at the University of Surrey on 8th December (Lara Harrup)
Year(s) Of Engagement Activity 2017
 
Description Practical training given to LSHTM MSc students 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Two-hour practical teaching session given to 12 MSc students at the London School of Hygiene and Tropical Medicine (LSHTM) on 17th November 2017 (Lara Harrup).
Year(s) Of Engagement Activity 2017
 
Description University of California Davis School of Veterinary Medicine 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact External Meeting at University of California Davis School of Veterinary Medicine, 16-18th October 2017. Talk given (Lara Harrup) on 'Tools and Resources for Arbovirus Epidemiology in the Genomic Era'. Meeting organised as part of the University of Liverpool BBSRC US Partnering Award: Vector-borne diseases in the UK & US: common threats and shared solutions (BB/N021916/1).
Year(s) Of Engagement Activity 2017