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

扁虱是一种广泛存在的体外寄生虫，以哺乳动物、鸟类的血液为食，有时还以爬行动物和两栖动物的血液为食。在全球范围内，虱子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，包括伯氏疏螺旋体细菌，这种细菌每年导致2000例莱姆病。在英国发现的其他扁虱传播的病原体包括吞噬细胞无形体、巴贝斯虫。以及鲁平病病毒，这些病毒会在农场和同伴动物中引起疾病，并可能影响人类。不断变化的气候和人类活动导致了硬蜱分布和活动的变化，增加了英国输入和建立新病原体和硬蜱物种的风险。在过去的20年里，在英国发现了赫氏立克次体、壁虱传播的脑炎病毒(TBEV)和卢文顺泰勒氏菌寄生虫。目前，英国是由英国卫生监督局(UKHSA)通过其壁虱监测计划(TSS)对壁虱和壁虱传播疾病(TBD)进行监测，而UKHSA稀有和进口病原体实验室(RIPL)是一个针对各种感染提供建议和诊断的专业中心。动植物卫生局(APHA)参与了对影响家畜的结核病的监测。监测和诊断目前基于扁虱鉴定、分子(聚合酶链式反应)和血清学试验以及组织学和细菌培养的使用。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对广泛的壁虱物种和壁虱传播的病原体进行高通量测试，以改进对影响人类和动物的结核病的监测。随着基因组学技术的进步，有一个独特的机会来提高大规模结核病监测的能力，降低成本，并获得有关扁虱和病原体遗传物质的信息。拟议的项目将有四个相关的目标：(1)完成英国主要扁虱物种的DNA序列，并创建用于监测扁虱及其携带的病原体的遗传条形码；(2)以高度有针对性的扩增子测序方法测试这些条形码，建立实验室和现场分析协议，筛选8,000个UKHSA TSS扁虱样本；(3)研究英国扁虱及其传播的病原体的遗传多样性，以及它们所捕食的扁虱、病原体和脊椎动物宿主之间的关系，并将这些数据与地理空间分析配对，以便更好地预防和针对干预措施；以及(4)发展硬蜱和硬虱传播病原体的基因组研究能力，包括开发生物信息学工具，供研究人员和利益攸关方，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，这些数据还将支持对结核病出现和传播的预测，并创建工具，及时检测任何输入的扁虱及其传播的病原体。

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.