Unravelling the aetiology of Stunting in UK Broiler Flocks through the use of novel microdissection and viral meta-transcriptomic sequencing tools

该项目解决的挑战是揭开英国肉鸡发育迟缓疾病的原因。自从商业肉鸡群在二战后实现工业化以来，发育迟缓一直是一个生产问题，但对于尼日利亚等低收入和中等收入国家的小生产者来说，发育迟缓也是一个问题，在尼日利亚，妇女经常饲养少量的鸡来补充家庭收入。发育迟缓问题有很多名称，包括传染性发育迟缓、跑步发育迟缓综合征和吸收不良疾病。它与尽管有足够的饲料但未能正常生长有关。鸟类通常在孵化后第二到第三周出现发育迟缓问题，但临床症状可能更早观察到。除了体重增加的减少--受严重影响的鸡只是其年龄潜在体重的一小部分--之外，可能还有其他迹象，如食欲改变、水样粪便、异常羽毛和肠炎。我们和其他小组有证据表明，发育迟缓是由感染性因素引起的：主要是病毒病因被怀疑，在AFBI分别使用特定的地方性病毒、肠道病毒、星状病毒和呼肠孤病毒的实验感染导致了在发育迟缓期间观察到的一些迹象，例如体重减轻或肠道粘膜损伤。其他小组也显示出一些发育迟缓的迹象，因为给鸟类接种了这些病毒和其他候选病毒的单一毒株，例如伯纳病毒；然而，没有一种病毒完全再现了发育迟缓综合征，与一种以上病毒的混合感染被认为是更有可能的病因。此外，这些病毒的不同毒株正在传播，已知它们的致病性差异很大，大多数可能是低致病性或没有致病性，因此在年轻、健康、未受影响的禽类中可能检测到高水平的这些病毒。疾病病因学的其他混杂因素包括母源抗体的存在、传播途径(从母鸡对其环境)以及禽类感染的年龄，因为年龄的增加似乎会产生抵抗力。所有这些因素也阻碍了对导致发育迟缓疾病的病毒的识别。该提案的具体目的是：1)识别在与发育迟缓疾病相关的皮损内活跃复制的一种或多种病毒，这些病毒存在于临床病例的许多类似皮损中。组织病理学和激光显微解剖将识别和切除病变，对病变中的核酸进行测序，以确定存在哪种病毒株(S)，其水平表明感染活跃。2)确认已鉴定的一种或多种病毒是发育迟缓的病原体；首先在实验室通过细胞和组织方法，其次通过使用已鉴定病毒的纯化分离株对健康鸡进行的挑战研究，这将证明发育迟缓疾病典型的标志性病变和相关的临床症状的发展。这些目标将通过使用最先进的成像和基因组方法，并通过与行业合作(Moy Park是英国最大的肉鸡生产商之一和圣大卫家禽团队，英国领先的家禽兽医实践)来实现。目前还没有商业疫苗来防止发育迟缓或对受影响的禽类进行特定的治疗，从而使受影响的禽类被扑杀。该项目的结果将提供导致发育迟缓的原因的证据，这将使兽医能够改进诊断和潜在的干预措施，并使疫苗公司能够开发适当的疫苗。

The challenge addressed by this project is to unravel the causes of stunting disease in UK broiler chickens. Stunting syndrome has been a production issue in commercial broiler flocks since they became industrialised after the second world war, but is also a problem for small producers in low and middle income countries, such as Nigeria, where women often raise small numbers of chickens to supplement the family income. The stunting problem has many names, including infectious stunting, runting stunting syndrome and malabsorption disease. It pertains to a failure to grow properly despite sufficient feed. Birds typically present with stunting problems around the second to third week post hatching, but clinical signs may be observable earlier. As well as the reduction in weight gain, which can be substantial with severely affected chickens only a fraction of their potential weight for age, there may be other signs such as altered appetite, watery droppings, abnormal feathering and enteritis. We and other groups have evidence that the stunting is caused by infectious agents: chiefly, viral aetiology is suspected and experimental infections at AFBI using specific strains of the endemic, enteric viruses, astroviruses and reoviruses separately have resulted in some of the signs observed during stunting, e.g. weight loss or lesions in the gut mucosa. Other groups have also demonstrated some of the signs of stunting from inoculating birds with single viral strains of these and other viral candidates, e.g. birnavirus; however, none have fully recreated the stunting syndrome, and co-infections with more than one viral agent are considered the more probable aetiology. Moreover, diverse strains of these viruses are in circulation which are known to vary widely in pathogenicity with the majority potentially of low or no pathogenicity and accordingly high levels of these virus may be detected in young, healthy, unaffected birds. Other confounding factors in attributing disease aetiology includes the presence of maternally-derived antibodies, route of transmission (from the hen versus their environment) and the age at which birds become infected, since increasing age appears to confer resistance. All these factors have also hampered the identification of the virus(es) responsible for stunting diseases.The specific aims of the proposal are to: 1) identify a virus or viruses that are actively replicating within the lesions associated with stunting disease and that are present in many similar lesions from clinical cases. Histopathology and laser microdissection will identify and excise lesions from which nucleic acids will be sequenced to determine which virus strain(s) is present at levels indicative of an active infection. 2) confirm that the virus or viruses identified are aetiological agents of stunting; firstly, by cellular and tissue-based methods in the laboratory and secondly, by challenge studies of healthy chickens using purified isolates of the identified virus(es), which will demonstrate the development of hallmark lesions and associated clinical signs typical of stunting disease. These objectives will be achieved through the use of state of the art imaging and genomic methodologies, and through collaboration with the Industry (Moy Park, which is one of UK's top broiler meat producers and St David's Poultry Team, the leading poultry veterinary practice in the country).Currently there are no commercial vaccines to prevent stunting or specific treatments for affected flocks so that affected birds are culled. The results of this project will provide evidence of the causal agents of stunting that will enable improved diagnostics and potential interventions for veterinarians, and for vaccine companies to develop appropriate vaccines.