GenES_VBD network (Genomic Epidemiology tools for the Surveillance of Vector Borne Diseases: applied to tick species, reservoirs, and pathogens

Ticks are widespread ectoparasites that feed on the blood of mammals, birds, and sometimes reptiles and amphibians. Globally, ticks can transmit a variety of pathogens to humans and animals. In the UK, they are responsible for spreading many pathogens including the bacteria Borrelia burgdorferi sensu lato, which is responsible for >2,000 cases of Lyme disease per year. Other tick-borne pathogens established in the UK include Anaplasma phagocytophilium, Babesia spp. and louping-ill virus, which cause disease in farm and companion animals, and potentially affecting humans.

The changing climate and human activities have contributed to changes in tick distribution and activity and increased the risk of importation and establishment of new pathogens and tick species into the UK. In the past 20 years, bacteria Rickettsia helvetica, tick-borne encephalitis virus (TBEV), and Theileria luwenshuni parasites have been detected in the UK.

Currently, the surveillance of ticks and tick-borne diseases (TBDs) in the UK is carried out by the UK Health Surveillance Agency (UKHSA) through their Tick Surveillance Scheme (TSS), while the UKHSA Rare and Imported Pathogens Laboratory (RIPL) is a specialist centre for advice and diagnosis for a wide range of infections. The Animal and Plant Health Agency (APHA) is involved in surveillance of TBDs that affect livestock.

Surveillance and diagnostics are currently based on tick identification and the use of molecular (PCR) and serological tests, as well as histology and bacterial cultures. All these approaches have limitations, including high-cost, and unsuitable for large-scale surveillance of multiple pathogens. Thus, new cost- effective tools are required for high throughput testing of a wide range of tick species and tick-borne pathogens to improve surveillance of TBDs that affect humans and animals.

With the advances in genomics technologies there is a unique opportunity to improve the capacity of large-scale TBDs surveillance at reduced cost and obtain information on the genetic material of tick and pathogens. The proposed project will have four related objectives: (1) to complete the DNA sequences of the main UK tick species and create genetic barcodes to be used for surveillance of ticks and pathogens they carry; (2) to test these barcodes in a highly targeted approach of amplicon sequencing, establish protocols for laboratory and field assays, and screen >8,000 UKHSA TSS tick samples; (3) to study the genetic diversity of UK ticks and pathogens they transmit, as well as the relationship between ticks, pathogens and vertebrate hosts they feed on, and pair this data with geospatial analysis to allow for better prevention and targeting of interventions; and (4) to develop capacity for the genomic investigation of ticks and tick-borne pathogens, including development of bioinformatics tools to be used by researchers and stakeholders such as UKHSA and APHA. This work will allow us to generate genetic epidemiological data which will also support forecasting of TBD emergence and spread, as well as create tools for timely detection of any imported ticks and pathogens they transmit.

Ticks are ectoparasites that feed on blood of a variety of vertebrates and transmit pathogens to humans and animals globally. In the UK, ticks are vectors and reservoirs of pathogens, such as Borrelia burgdorferi s.l., which is responsible for >2k cases of Lyme disease each year. Other tick-borne pathogens established in the UK include Anaplasma phagocytophilium, Babesia spp. and louping-ill virus, affecting farm and companion animals. Changing climate and human activities have increased the risk of importation and establishment of new tick species and pathogens, such as tick-borne encephalitis virus and Theileria luwenshuni that were detected in UK in the last decade.
Tick-borne disease (TBD) surveillance in the UK is carried out by the UKHSA through their Tick Surveillance Scheme (TSS) and Rare and Imported Pathogens Laboratory, and the Animal and Plant Health Agency (APHA). With advances in genomics-based technologies and their reducing costs, there is a unique opportunity to improve the capacity of large-scale surveillance of TBDs. The aim of our work is to enhance existing UK tick and pathogen surveillance through application of genomic methods, including protocols to determine species and geographic origin, and detect presence of pathogens, generating genetic epidemiological data to support forecasting of TBD emergence and spread. The proposed project will have four related objectives, to: (1) identify genetic barcodes for surveillance of ticks and pathogens; (2) validate the barcodes for amplicon sequencing, screen TSS ticks, and establish protocols for laboratory and field assays; (3) perform a geospatial-phylo-genomic-epidemiological analysis across ticks, their pathogens and hosts; (4) develop capacity in genomic investigation of ticks and pathogens, including through sharing informatics tools for use by researchers and stakeholders for decision making. Our work will also provide a template for the genomics surveillance of other vector borne infections.