Selection Versus Mutation: Reducing the Risk of Vaccine Reversion

选择与突变：降低疫苗回复的风险

• 批准号: BB/L003988/1
• 负责人: Paul Britton
• 金额: $ 43.17万
• 依托单位: The Pirbright Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL003988%2F1
• 关键词: Selection; Versus; Mutation; Reducing; Risk

Vaccination against numerous endemic pathogens is an essential component of the poultry industry. Without these vaccines chickens would succumb to infection at an early age reducing the productivity of the industry well below sustainable levels. IBV is an endemic virus that causes severe disease outbreaks in chickens worldwide. Effective and economically viable vaccines against IBV are available and mainly produced from pathogenic virus strains by passing in eggs approximately one hundred times. During these passages the virus accumulates multiple sequence variations from the original pathogenic sequence. This ultimately leads to attenuation of the virus and the production of a live attenuated vaccine. These vaccines have lost their ability to cause disease but still elicit a protective immune response in the chicken, thus protecting the bird from future infections. However, as these are live viruses the potential for to revert back to a pathogenic form is considerable considering the few sequence changes between wild and vaccine strains.Despite the importance of these vaccines to the poultry industry and the risk of reversion, the processes that occur and the selective forces that drive virus attenuation during egg passage are unknown. Importantly, the differential contribution of virus sequence mutation compared to the selection of minor variants already present in the virus population has not been determined. Understanding these basic processes is essential to the development of future vaccines to reduce the threat of reversion.This study will use passaged pathogenic IBV strains produced in the same way as vaccines. In parallel we will use a unique system that allows us to passage a single virus clone rather than a mixed virus population. Using contemporary deep sequencing technology we will study the molecular changes that occur at fine resolution during the attenuation process. This will for the first time reveal how a mixed population of virus changes during vaccine manufacture and the extent to which individual viruses can mutate. These results will then inform a series of studies that manipulates the forces that drive virus change. The first will use IBV strains that contain a protein from another strain that influences the immune response in the chicken, and the second will use viruses that mutate much faster than wild type viruses. By passaging and deep sequencing these viruses in the same way as the wild type viruses, we will understand how different forces drive virus sequence mutation. These recombinant passaged viruses will then be tested to determine if this process has led to attenuation and also if they maintain the potential to infect other chickens that are exposed to vaccinated birds. Ultimately this research will reveal how IBV is attenuated by egg passage and identify key regions of the genome that prevent the virus from causing disease but do not impair its potential as a vaccine. Moreover, we will further develop our understanding of how different pressures influence the attenuation process and potentially identify ways to improve the process of vaccine design by engineering attenuated viruses. By understanding and manipulating the processes that govern virus attenuation and vaccine production we aim to identify ways of reducing the danger of vaccine strains reverting and causing damaging disease outbreaks.

针对多种地方性病原体的疫苗接种是家禽业的重要组成部分。如果没有这些疫苗，鸡就会在很小的时候就死于感染，从而使该行业的生产力大大低于可持续水平。 IBV 是一种地方性病毒，可导致全世界鸡群爆发严重疾病。有效且经济上可行的 IBV 疫苗是可用的，并且主要是通过在鸡蛋中传递大约一百次的致病病毒株来生产的。在这些传代过程中，病毒积累了原始致病序列的多个序列变异。这最终导致病毒减毒并生产减毒活疫苗。这些疫苗已经失去了引起疾病的能力，但仍能在鸡体内引起保护性免疫反应，从而保护鸡免受未来的感染。然而，由于这些是活病毒，考虑到野生毒株和疫苗毒株之间的序列变化很少，恢复到致病形式的可能性相当大。尽管这些疫苗对家禽业很重要并且存在恢复的风险，但发生的过程在鸡蛋传代过程中驱动病毒减毒的选择力尚不清楚。重要的是，与病毒群体中已存在的微小变体的选择相比，病毒序列突变的差异贡献尚未确定。了解这些基本过程对于开发未来疫苗以减少回复威胁至关重要。这项研究将使用以与疫苗相同的方式生产的传代致病性IBV毒株。与此同时，我们将使用一个独特的系统，使我们能够传代单个病毒克隆而不是混合病毒群体。利用当代深度测序技术，我们将研究衰减过程中以精细分辨率发生的分子变化。这将首次揭示疫苗制造过程中混合病毒群体如何变化以及单个病毒的突变程度。这些结果将为一系列操纵驱动病毒变化的力量的研究提供信息。第一个将使用含有来自另一种菌株的蛋白质的 IBV 菌株，该蛋白质会影响鸡的免疫反应，第二个将使用比野生型病毒突变快得多的病毒。通过以与野生型病毒相同的方式对这些病毒进行传代和深度测序，我们将了解不同的力量如何驱动病毒序列突变。然后将对这些重组传代病毒进行测试，以确定该过程是否导致了减毒，以及它们是否仍然有可能感染其他接触过疫苗接种的鸡的鸡。最终，这项研究将揭示IBV如何通过卵传代减弱，并确定基因组的关键区域，这些区域可以防止病毒引起疾病，但不会削弱其作为疫苗的潜力。此外，我们将进一步加深对不同压力如何影响减毒过程的理解，并可能找到通过设计减毒病毒来改进疫苗设计过程的方法。通过了解和操纵控制病毒减毒和疫苗生产的过程，我们的目标是找到减少疫苗株恢复和导致破坏性疾病爆发的危险的方法。

项目成果

SiNPle: Fast and Sensitive Variant Calling for Deep Sequencing Data.

SiNPle：快速、灵敏的深度测序数据变体调用。

• DOI: http://dx.10.3390/genes10080561
• 发表时间: 2019
• 期刊: Genes
• 影响因子: 3.5
• 作者: Ferretti L

Genomics and outbreaks: foot and mouth disease.

基因组学和爆发：口蹄疫。

• DOI: http://dx.10.20506/rst.35.1.2426
• 发表时间: 2016
• 期刊: Revue scientifique et technique (International Office of Epizootics)
• 作者: Freimanis GL

Identification of Amino Acids within Nonstructural Proteins 10 and 14 of the Avian Coronavirus Infectious Bronchitis Virus That Result in Attenuation In Vivo and In Ovo.

禽冠状病毒传染性支气管炎病毒非结构蛋白 10 和 14 中导致体内和卵内减毒的氨基酸的鉴定。

• DOI: http://dx.10.1128/jvi.02059-21
• 发表时间: 2022
• 期刊: Journal of virology
• 作者: Keep S

Whole-Genome Sequencing Protocols for IBV and Other Coronaviruses Using High-Throughput Sequencing.

使用高通量测序的 IBV 和其他冠状病毒的全基因组测序方案。

• DOI: http://dx.10.1007/978-1-0716-0900-2_5
• 发表时间: 2020
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Freimanis GL

Partial purification of IBV and subsequent isolation of viral RNA for next-generation sequencing.

部分纯化 IBV 并随后分离病毒 RNA 以进行下一代测序。

• DOI: http://dx.10.1007/978-1-4939-2438-7_11
• 发表时间: 2015
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Keep SM