Genomic epidemiological determination of routes of pathogenic virus transmission between farmed salmon

养殖鲑鱼间致病病毒传播途径的基因组流行病学测定

• 批准号: BB/W006294/1
• 负责人: Sarah Hill
• 金额: $ 55.08万
• 依托单位: Royal Veterinary College
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FW006294%2F1
• 关键词: Genomic; epidemiological; determination; routes; pathogenic

Viruses that cause disease and death in farmed salmon harm the UK's economy, increase the carbon and environmental footprint of production, and reduce fish welfare. Two viruses, called piscine myocarditis virus (PMCV) and infectious salmon anaemia virus (ISAV) are particularly damaging. For every eight salmon that die of known causes on fish farms, one death is caused by PMCV. ISAV is less commonly detected in the UK, and the UK is currently considered free of the disease. However, introductions of ISAV have been shown to nearly destroy entire salmon industries in other countries and therefore protecting against new outbreaks remains critical as the UK expands salmon production to meet growing global demand. Despite the severe problems caused by these viruses, we do not fully understand how they transmit between farms. Our lack of understanding of how viruses enter and persist on farms has prevented action that can improve disease control.We propose to use virus genomic sequencing and genomic analyses to determine the routes of ISAV and PMCV transmission, and how and where pathogenic lineages emerge. Many viruses evolve very rapidly, and acquire genetic changes as they transmit between hosts. Using the evolved patterns of virus genetic changes to reconstruct ancestral relationships between viruses can be used to track how they transmit. Generated virus genomes additionally provide important information on the genetic basis for disease severity, and how pathogenic strains emerge. This approach has been widely used in public health to understand disease in humans, but opportunities to study disease transmission in farmed fish are being missed. We will answer several key questions that will improve our understanding of how to eliminate transmission. Fish are moved between farms as they grow, from egg and progeny in tanks, to inland freshwater sites as juveniles, and finally to the sea at adulthood. Firstly, we will reconstruct transmission to determine whether each virus tends to transmit between farms at the same production stage, or between different stages. This would indicate where biosecurity improvements are best focused. Secondly, we will determine what characteristics of a farm make it more likely to become infected or transmit these viruses with other farms. Identified characteristics could be used to improve surveillance for viruses at certain points in the fish supply chain, leading to more rapid detection and control if viruses are present. Thirdly, we will determine whether wild fish are a source of infection of PMCV, or whether they only rarely become infected when they come into contact with infected farms. The distinction is important to determine whether wild fish can easily infect fish on farms, or whether in contrast wild fish must be better protected to prevent establishment of virus transmission within wild populations. Finally, we seek to understand how genetic changes in the virus lead to more or less severe disease. This could be used to improve genetic 'early warning systems' for risk of disease emergence in fish or improve vaccinations, and are more broadly useful to understand how related viruses evolve and cause disease in other species. The approaches that we use in this research will also be broadly applicable to viral diseases, improving our ability to rapidly respond to new viral outbreaks in humans and other animalsTogether, our results will contribute to reducing disease amongst farmed salmon. This will lead to improved fish welfare, a more sustainable industry, cheaper cost of fish to the consumer because of reduction in loss, and greater economic value of the industry. Our results will be valuable to the UK, where salmon is the second most valuable food export, but also to producers and consumers in other markets worldwide.

在养殖鲑鱼中引起疾病和死亡的病毒损害了英国的经济，增加了生产的碳和环境足迹，并降低了鱼类福利。两种病毒，称为鱼心肌炎病毒（PMCV）和传染性鲑鱼贫血病毒（ISAV）是特别有害的。在养鱼场中，每八条死于已知原因的鲑鱼中，就有一条是由PMCV引起的。ISAV在英国不太常见，英国目前被认为没有这种疾病。然而，ISAV的引入几乎摧毁了其他国家的整个鲑鱼产业，因此，随着英国扩大鲑鱼产量以满足不断增长的全球需求，防止新的疫情仍然至关重要。尽管这些病毒造成了严重的问题，但我们并不完全了解它们如何在农场之间传播。我们缺乏了解病毒如何进入并持续在农场阻止了行动，可以提高疾病control.We建议使用病毒基因组测序和基因组分析，以确定ISAV和PMCV的传播途径，以及如何和在哪里致病谱系出现。许多病毒进化非常迅速，并在宿主之间传播时获得遗传变化。利用病毒遗传变化的进化模式来重建病毒之间的祖先关系，可以用来追踪它们是如何传播的。生成的病毒基因组还提供了关于疾病严重程度的遗传基础以及致病菌株如何出现的重要信息。这种方法已被广泛用于公共卫生领域，以了解人类疾病，但正在错过研究养殖鱼类疾病传播的机会。我们将回答几个关键问题，这将提高我们对如何消除传播的理解。鱼类在成长过程中在养殖场之间移动，从水箱中的卵和后代，到内陆淡水地区的幼鱼，最后到成年后的大海。首先，我们将重建传播，以确定每种病毒是倾向于在同一生产阶段的农场之间传播，还是在不同阶段之间传播。这将表明生物安保改进的最佳重点。其次，我们将确定一个农场的哪些特征使它更有可能被感染或将这些病毒传播给其他农场。已确定的特征可用于改善鱼类供应链中某些环节的病毒监测，从而在病毒存在时更快地检测和控制。第三，我们将确定野生鱼是否是PMCV的感染源，或者它们是否在接触受感染的农场时很少被感染。这种区别对于确定野生鱼类是否容易感染养殖场的鱼类，或者相反，野生鱼类是否必须得到更好的保护，以防止在野生种群中建立病毒传播是很重要的。最后，我们试图了解病毒的遗传变化如何导致或多或少的严重疾病。这可用于改善鱼类疾病出现风险的遗传“早期预警系统”或改善疫苗接种，并更广泛地用于了解相关病毒如何进化并在其他物种中引起疾病。我们在这项研究中使用的方法也将广泛适用于病毒性疾病，提高我们对人类和其他动物中新病毒爆发的快速反应能力，我们的研究结果将有助于减少养殖鲑鱼的疾病。这将导致改善鱼类福利，一个更可持续的行业，由于减少损失，消费者的鱼成本更低，该行业的经济价值更大。我们的研究结果将对英国有价值，鲑鱼是第二大最有价值的食品出口，但也对全球其他市场的生产者和消费者有价值。