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

蜱是广泛分布的体外寄生虫，以哺乳动物，鸟类，有时爬行动物和两栖动物的血液为食。在全球范围内，蜱可以将各种病原体传播给人类和动物。在英国，它们负责传播许多病原体，包括细菌Borrelia burgdorferi sensu lato，每年造成超过2，000例莱姆病。在英国建立的其他蜱传病原体包括嗜吞噬细胞无形体、巴氏杆菌属。以及导致农场和伴侣动物疾病并可能影响人类的louping-ill病毒。不断变化的气候和人类活动导致蜱虫分布和活动发生变化，并增加了新病原体和蜱虫物种进入英国的风险。在过去的20年里，在英国发现了瑞士立克次体、蜱传脑炎病毒（TBEV）和鲁文舒尼泰勒虫寄生虫。目前，英国蜱虫和蜱传疾病（TBD）的监测由英国卫生监督局（UKHSA）通过其蜱虫监测计划（TSS）进行，而UKHSA罕见和进口病原体实验室（RIPL）是一个专业中心，为各种感染提供咨询和诊断。动植物卫生署参与监测影响牲畜的TBD，目前的监测和诊断是基于蜱虫鉴定和使用分子（PCR）和血清学测试，以及组织学和细菌培养。所有这些方法都有局限性，包括成本高，不适合大规模监测多种病原体。因此，需要新的具有成本效益的工具来高通量测试广泛的蜱物种和蜱传播的病原体，以改善对影响人类和动物的TBD的监测。随着基因组学技术的进步，有一个独特的机会，以降低成本，提高大规模的TBD监测能力，并获得有关蜱和病原体的遗传物质的信息。拟议项目将有四个相关目标：（1）完成英国主要蜱虫物种的DNA序列，并创建用于监测蜱虫及其携带的病原体的遗传条形码;（2）以高度靶向的扩增子测序方法测试这些条形码，建立实验室和现场检测方案，并筛选> 8，000个UKHSA TSS蜱虫样本;（3）研究英国蜱虫及其传播的病原体的遗传多样性，以及蜱虫、病原体和它们所食脊椎动物宿主之间的关系，并将这些数据与地理空间分析相结合，以便更好地预防和针对干预措施;和（4）发展蜱和蜱传病原体基因组调查的能力，包括开发生物信息学工具，供研究人员和利益相关者（如UKHSA和APHA）使用。这项工作将使我们能够生成遗传流行病学数据，这也将支持预测TBD的出现和传播，并创建工具，以及时检测任何进口蜱及其传播的病原体。

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.