Beyond the consensus: defining the significance of foot-and-mouth disease viral sequence diversity

口蹄疫是由一种含有RNA基因组的小病毒（FMDV）引起的。与大多数其他RNA病毒一样，FMDV的复制机制在复制过程中复制基因组时会出错。因此，病毒进化非常迅速，能够迅速适应不同的环境压力。在2001年和2007年爆发在英国，我们利用这些属性的指纹FMDV从现场样品中回收，以显示如何在不同的农场收集的病毒相互关联。这些数据为协助追踪流行病提供了宝贵的信息，并在2007年实时用于支持环境、食物和农村事务部的控制和根除政策。这种类型的分析很可能会被广泛用于支持英国（或欧洲其他地方）未来的任何口蹄疫入侵。然而，我们目前对这些数据的解释受到我们对精细尺度过程的理解的限制，这些精细尺度过程是病毒在牛到牛（或动物到动物）水平传播期间观察到的遗传变化的基础。该项目的目的是使用“下一代”测序技术首次揭示样本中存在的复杂病毒混合物，这些病毒是FMDV精细进化的起始材料。我们已经进行了初步的实验，以优化和评估这种方法使用的样品收集从一个单一的奶牛，已实验接种口蹄疫病毒。这些数据表明，我们能够测量感染动物足部病变中存在的非常罕见的遗传变异的频率。这些变异体中的许多代表了以前使用常规方法未检测到的遗传中间体。因此，我们得出结论，这种新的测序方法非常适合揭示复杂病毒群体的精细亚结构，并将成为量化口蹄疫病毒高分辨率进化动力学的有价值的工具。在这个项目中，我们的目标是扩展这种方法，从更广泛的样本中生成数据，这些样本已经从以前的口蹄疫现场爆发中收集（并存档），并从受控实验传播研究中获得，并开发量化传播对遗传多样性影响的模型。除了提高我们对FMDV进化方式的理解外，我们预计该项目的发现将广泛应用于其他急性作用病毒感染的传播生物学，包括人类和兽医重要性病毒，如猪瘟，猪水泡病病毒，狂犬病病毒，流感和冠状病毒样（SARS）病毒。

Foot-and mouth disease is caused by a small virus (FMDV) which has an RNA genome. In common with most other RNA viruses, the replication machinery of FMDV makes errors when it copies the genome during replication. As a consequence, the virus evolves very rapidly and can quickly adapt to different environmental pressures. During the 2001 and 2007 outbreaks in the UK, we exploited these properties to finger-print FMDVs recovered from field samples to show how viruses collected on different farms were related to each other. These data provide valuable information to assist in epidemiological tracing and were used in real-time in 2007 to support Defra's control and eradication policy. It is likely that this type of analysis will be widely used to support any future incursions of FMD in the UK (or elsewhere in Europe). However, our current interpretation of these data is limited by our understanding of the fine-scale processes that underpin the genetic changes that are observed during transmission of the virus at the herd-to-herd (or animal-to-animal) level. The aim of this project is to use a 'next-generation' sequencing technology to reveal, for the first time, the complex mixture of viruses that are present within samples and are the starting material for fine-scale evolution of FMDV. We have conducted preliminary experiments to optimise and evaluate this method using a samples collected from a single cow that had been experimentally inoculated with FMDV. These data demonstrate that we are able to measure the frequency of even very rare genetic variants that exist in feet lesions from an infected animal. Many of these variants represent genetic intermediates that were previously undetected using conventional methods. We therefore, conclude that this new sequencing methodology is well-suited to revealing the fine substructure of complex viral populations and will be a valuable tool to quantify the high-resolution evolutionary dynamics of FMDV. During this project, we aim to extend this approach to generate data from a wider range of samples that have already been collected (and archived) from previous field outbreaks of FMD, and from controlled experimental transmission studies and develop models that quantify the effects of transmission on genetic diversity. In addition to improving our understanding of the way that FMDV evolves, we anticipate that the findings from this project will have broad application to the transmission biology of other acutely acting viral infections including viruses of human and veterinary importance such as classical swine fever, swine vesicular disease virus, rabies virus, influenza and corona-like (SARS) viruses.