Using a 'Vaccinomics' Approach to Characterise FMDV Evolution under Vaccine Selection

动物健康是BBSRC的战略重点，对粮食安全和经济作出贡献。我们通过生产更有效的疫苗制定成功的动物疾病干预战略的工作是保护我们牲畜的有力战略，牛瘟等病毒已经成功根除。口蹄疫病毒（FMDV）对牲畜具有重大的社会经济影响，通过接种疫苗消灭/控制其爆发至关重要。许多RNA病毒（如FMDV）以异质种群存在，称为准种，由相关但不相同的基因组组成。这种复杂性是由于它们的高复制率、庞大的种群规模和容易出错的复制，目前的估计预测在每个病毒复制周期中会发生一个核苷酸变化（Klein等人，2009）。这种进化的可塑性对设计有效疫苗的策略造成了重大限制，这些疫苗可以防止大范围不断变化的流行野毒株。此外，可能在传播和准种进化中发挥重要作用并可能对疫苗稳定性和效力（混合群体疫苗）产生严重影响的FMDV的次要变异仍未得到描述。因此，系统调查影响口蹄疫疫苗质量的因素，包括描述小变异、准种动态、异质性和引起宿主反应，对于建立针对口蹄疫疫情的强有力的疫苗接种制度至关重要。高通量技术和大规模数据集，如基因组学、转录组学和蛋白质组学，正越来越多地用于疫苗开发和疫苗安全性研究，因此出现了疫苗组学这一术语（Luciani等，2012年）。在这里，我们采用高通量测序来解决三个目标：1。准确、快速获取来自不同地理区域的不同FMDV毒株的全基因组序列（WGS），以进一步了解FMDV准种驱动免疫逃逸和促进病毒持久性或载体状态的分子和进化机制。（即致力于开展口蹄疫病毒预防规划）检测少数变异和逃逸突变体（低至0.1%）并确定其特征，以了解疫苗的异质性及其对疫苗质量的影响（即致力于改进/更强大的疫苗接种计划）。3. 确定宿主对口蹄疫疫苗接种的转录组反应，了解宿主与病原体/疫苗接种之间的相互作用，这对提供保护很重要（即努力制定完善的疫苗接种计划）。高通量技术还将用于描述和评估疫苗质量标准的各个方面（即种子批次和外来病原体的同质性）。

Contributing to food security and our economy, animal health is a strategic priority of the BBSRC. Our work on the development of successful animal-disease intervention strategies by producing more effective vaccines is a powerful strategy to protect our livestock, with viruses such as rinderpest already successfully eradicated. Foot-and-mouth disease virus (FMDV) has significant socio-economic effects on livestock and its eradication/outbreak control through vaccinations is of prime importance. Many RNA viruses such as FMDV exist as heterogeneous populations known as quasispecies, comprising related but non-identical genomes. Such complexity is due to their high replication rate, large population size and error-prone replication with current estimates predicting one nucleotide change occurring during each cycle of virus replication (Klein et al, 2009). Such evolutionary plasticity places significant limitations upon the strategies for the design ofefficacious vaccines that can protect against a wide range of constantly changing circulating field strains. Moreover, minor variants of FMDV, that may have an important role in transmission and quasispecies evolution with potentially serious effects on vaccine stability and efficacy (mixed-population vaccines), remain uncharacterised. Systematic investigations into the factors that effect FMDV vaccine quality in terms of characterising minor variants, quasispecies dynamics, heterogeneity and invoking a host-response are therefore critical in establishing a robust vaccination regime against FMDV outbreaks.High throughput technologies and large-scale datasets such as genomics, transcriptomics and proteomics are increasingly being exploited within vaccine development and vaccine safety research, hence the term Vaccinomics (Luciani et al, 2012). Here we employ high-throughput sequencing to address three objectives: 1. Accurately and rapidly obtain whole genomesequences (WGS) of different FMDV strains from different geographical regions to further understanding of the molecular and evolutionary mechanisms employed by FMDV quasispecies that drive immune escape and contribute to viral persistence or carrier states. (i.e. working towards an FMDV prevention program) 2. Detect and characterise minority variants and escape mutants (as low as 0.1%) to understand the heterogeneity of vaccines and the effects that this has on vaccine quality (i.e. working towards an improved/more robust vaccination program). 3. Determine the host's transcriptomic response to FMDV vaccinations, to understand the interactions between host and pathogen/vaccination that are important for providing protection (i.e. working towards a refined vaccination program). High-throughput technologies will also be used to characterise and assess aspects of vaccine quality criteria (i.e. homogeneity of seed lots and adventitious pathogens).