Investigating Host and Viral Factors for Improved Design of Future Live Attenuated Vaccines for IBV

针对地方性病原体的疫苗接种是家禽业的一个重要组成部分，如果没有疫苗接种，鸡将在幼年时受到感染。这将降低生产力，使粮食安全超出可持续水平。传染性支气管炎病毒（IBV）是一种冠状病毒，会导致鸡呼吸道疾病，使它们更容易受到细菌感染。感染后，它们的体重下降，产的优质卵也减少。据估计，全球IBV发病率减少10%将为家禽业带来6.54亿英镑的价值。因此，从福利和经济两方面考虑，一种有效的IBV疫苗至关重要。针对IBV的最佳疫苗策略是“减毒活”型，这意味着使用一种减弱的致病病毒给鸡接种疫苗，从而产生良好的免疫力。这些疫苗是由致病（致病性）病毒在鸡蛋中生长多达100次而产生的，在此期间可能发生多次基因组变化。我们对这个过程的理解是有限的。虽然这些疫苗已经失去了引起症状的能力，但它们仍然保留了在鸡中诱导保护性免疫反应的能力，从而保护它们免受疾病的侵害。然而，据报道，一些疫苗毒株发生了进化，在接种疫苗后引起禽群疾病暴发。这种情况发生在疫苗病毒基因组发生变化时，并且存在一种风险，即它们可能重新获得致病能力（逆转），在接种疫苗的禽类中产生疾病，即疫苗病毒引起新的疫情。更好地了解疫苗病毒如何被削弱以及疫苗接种后宿主压力如何驱动逆转是设计更稳定疫苗的关键。在先前的一个项目（BB/L003988/1）中，通过在鸡蛋中传代来减弱2种IBV病毒（一种商业疫苗和一种实验室适应菌株），以确定病毒如何变化。我们每隔10代对这些病毒进行深度测序，以了解它们是如何变化的。我们从现有的数据集中知道，弱化病毒和致病性病毒之间有一些共同的变化。我们还知道，有些更改是每种类型所独有的。此外，基因序列的变化还受传代过程中限制多样性和稀释因子等因素的影响。我们不知道这些变化将如何影响疫苗接种后的逆转。该项目的总体目标是对鸡接种IBV疫苗时的病毒动力学-宿主相互作用进行详细描述，以获得对病毒生物学和宿主反应的重要见解。这将回答3个研究问题：1。在这个弱化过程中，病毒是否发生了变化，可用于改进未来的疫苗？疫苗病毒的基因组在接种鸡后是如何变化的，这些变化是否使它们更容易引起逆转？哪些宿主基因被表达，它们是否有助于驱动疫苗病毒在鸡体内进化？我们将使用深度学习来识别病毒基因组在弱化过程中的基因组模式。我们将描述疫苗病毒在接种鸡后如何变化，将变化与致病性病毒的变化进行比较，以测量逆转的可能性。我们将描述疫苗接种后细胞基因表达的特征，并使用机器学习来识别驱动疫苗病毒基因组变化的细胞反应。最后，我们将结合数据集并使用机器学习来预测哪些序列变化在削弱病毒和恢复过程中是重要的。这些预测将被重新插入病毒中，并测量它们对鸡细胞的影响。这项研究将确定与发生和逆转的可能性有关的基因组变化，并揭示它们在接种疫苗后将如何变化。这些结果将进一步加深我们对衰减期间和接种疫苗后影响病毒基因组的过程的理解，可用于未来的下一代疫苗。

Vaccination against endemic pathogens is an essential component of the poultry industry, without which chickens would become infected at an early age. This would reduce productivity and push food security beyond sustainable levels. Infectious bronchitis virus (IBV) is a coronavirus that causes respiratory disease in chickens, making them more susceptible to bacterial infections. After infection, they achieve lower weights and produce fewer high-quality eggs. It has been estimated that a 10% reduction in IBV incidence globally would be worth £654million to the poultry industry.An effective vaccine to IBV is therefore critical for both welfare and economic reasons. The best vaccine strategies for IBV are "live attenuated" types, meaning a weakened form of the disease-causing virus is used to vaccinate chickens, generating good immunity. These vaccines are produced by growing disease-causing (pathogenic) viruses in eggs up to one hundred times, during which multiple genome changes can occur. Our understanding of how this process works is limited. Whilst these vaccines have lost their ability to cause symptoms, they still retain the ability to induce protective immune responses in chickens, thereby protecting them from disease. However, some vaccine strains have been reported to evolve, causing outbreaks of disease in flocks after vaccination. This occurs as vaccine virus genomes change and there is a risk, they may regain their pathogenic capability (reversion), producing disease in vaccinated birds i.e. the vaccine virus causes new outbreaks. Understanding better how both vaccine viruses are weakened and the host pressures after vaccination drive reversion are key to designing more stable vaccines.In a previous project (BB/L003988/1) 2 IBV viruses were weakened (a commercial vaccine and a lab-adapted strain) by passaging in eggs to identify how the viruses changed. We deep sequenced these viruses every 10 passages to understand how they change. We know from existing datasets that some changes are shared between both weakened and pathogenic viruses. We also know that some changes are exclusive to each type. Moreover, sequence changes are influenced by factors including restricted diversity and dilution factors during egg passaging. We do not know how these changes will impact reversion after vaccination.The overall aim of the project is to produce a detailed profile of the viral dynamics-host interactions of IBV vaccination in chickens to gain major insights into the virus biology and host responses. This will answer 3 research questions:1. Are there changes in the virus during this weakening process that can be used to improve future vaccines?2. How do vaccine virus's genomes changes after vaccination into chickens and do these changes make them more likely to cause reversion?3. What host genes are expressed, and do they help drive vaccine viruses to evolve in chickens?We will use deep learning will identify genomic patterns in viral genomes during the weakening process. We will characterise how vaccine viruses change after vaccination into chickens, comparing changes to those in pathogenic viruses, to measure the likelihood of reversion. We will characterise cellular gene expression, after vaccination and use machine learning to identify cellular responses driving changes in the vaccine virus genomes. Finally, we will combine datasets and use machine learning to make predictions on which sequence changes are important in the processes of weakening viruses, and reversion. These predictions will be re-inserted back into a virus and their impact on chicken cells measured.This research will identify genome changes involved in the occurrence and likelihood of reversion and reveal how they will change post-vaccination. These results will further our understanding of processes impacting virus genomes both during attenuation and after vaccination, that can be used in future next generation vaccines.