20-EEID US-UK Modelling reassortment at the cellular, clinical, and phylogenetic level in emerging Bunyaviruses

基因组分割对于病毒基因表达调控和RNA组装成新生病毒粒子具有重要意义。它还创造了重新分类的可能性：在共同感染同一细胞的病毒之间交换完整的基因片段。重组在数量上不同于分子内重组，因为它允许从单个共同感染的细胞中出现许多不同的基因类型。片段不仅增强了遗传多样性，而且由于重组在种群规模上成功的罕见情况，它在许多片段病毒的进化史中也发挥着独特的作用。通过从布尼亚病毒目重新分类出现一种新病毒的一个显著例子是阿里病毒。对于流感病毒(IAV)这一最具特征的节段性病毒，重新分类促进了1957、1968和2009年大流行毒株的形成。在世卫组织2018年研发蓝图列为迫切需要加快研究的突发公共卫生事件的七种疫情易发疾病中，有三种是本雅氏病毒。因此，该项目的首要假设是，节段病毒的重新分类不仅在推动它们的多样化和进化方面发挥着重要作用，而且还显著改变了它们的生态和传播动态。具体地说，我们的目标是1)为一系列分段病毒建立细胞内生命周期的数学模型，并与体外实验一起首次量化它们的病毒复制动力学和重新分类频率，以及2)开发标准化的测序方案，以及新的系统发育方法，以量化克里米亚-刚果出血热病毒(CCHFV)重新分类的进化和流行病学影响。该项目将建立一个生物库，存储土耳其和塔吉克斯坦CCHFV主要流行区的临床和现场样本。我们将利用临床和现场数据，以便我们的方法和结果有可能为控制战略和预测暴发风险提供信息。在该项目中开发的量化方法将有助于索尔维洛等人倡导的“一个健康”方法。用于CCHFV。我们的目标是开发新的数学和系统动力学方法，在细胞和流行病水平上量化分段布尼亚病毒的重新分类频率和适合度。这将加强我们对土耳其和塔吉克斯坦CCHFV演变和流行病学的了解。为了实现这一目标，这个美英合作项目汇集了系统发育、数学建模、BSL-3和BSL-4能力方面的专业知识，以及土耳其和塔吉克斯坦的现场和临床专业知识，可以直接获取大量人类、动物宿主和病媒样本。我们将量化重组模式，将节肢动物和脊椎动物细胞系中选定的布尼亚病毒的数学模型与体外实验结合起来。统计推断将使我们能够估计每个重组宿主和细胞宿主的基本繁殖数量。在种群水平上，我们将设计DNA测序和系统动力学方法来剖析节段性病毒的进化和传播历史。因此，我们将在土耳其和塔吉克斯坦收集的现场数据的系统发育分析将关键地评估CCHFV的点突变、重组和重新分类的卷积。在该项目中采用和开发的系统动力学方法，以及现场数据，将使我们能够将这些进化过程与CCHFV暴发的宿主切换、时间和地理模式联系起来。利用来自土耳其和塔吉克斯坦的临床信息和数据，我们将对CCHFV医院传播的数学模型进行参数化，为公共卫生决策提供信息。虽然我们专注于布尼亚病毒科，特别是CCHFV，但我们的定量方法将适用于其他与公共卫生密切相关的节段病毒。

Genome segmentation has important implications for viral gene expression control and RNA assembly into nascent virions. It also creates the potential for reassortment: the exchange of intact gene segments between viruses that coinfect the same cell. Reassortment is quantitatively different from intramolecular recombination in that it allows many distinct genotypes to emerge from a single coinfected cell. Not only does segmentation enhance genetic diversification but it also plays a unique role in the evolutionary history of many segmented viruses due to the rare occasions when a reassortant is successful at the population scale. A striking example of the emergence of a novel virus through reassortment from the Bunyavirales is that of Ngari virus. For influenza (IAV), the best characterised segmented virus, reassortment has facilitated the formation of pandemic strains in 1957, 1968 and 2009. Out of seven epidemic-prone diseases prioritised by the WHO 2018 R&D Blueprint as public health emergency with an urgent need for accelerated research, three are Bunyaviruses. Thus, the overarching hypothesis of this project is that reassortment of segmented viruses plays a major role not only to drive their diversification and evolution, but to dramatically alter their ecology and transmission dynamics. Specifically, we aim to 1) develop mathematical models of the intracellular life cycle for a family of segmented viruses and together with in vitro experiments quantify for the first time their viral replication dynamics and reassortment frequencies, and 2) develop standardised protocols for sequencing, as well as novel phylogenetic methods to quantify the evolutionary and epidemiological implications of reassortment for Crimean-Congo hemorrhagic fever virus (CCHFV). A biobank with clinical and field samples from key CCHFV endemic regions in Turkey and Tajikistan will be set up in this project. Clinical and field data will be leveraged so that our methods and results have the potential to inform control strategies and predict outbreak risk. The quantitative methods developed in this project will contribute to the One Health approach advocated by Sorvillo et al. for CCHFV. Our goal is to develop novel mathematical and phylodynamic methods to quantify, at the cellular and the epidemic levels, reassortment frequency and fitness for segmented Bunyaviruses. This will enhance our understanding of CCHFV evolution and epidemiology in Turkey and Tajikistan. To achieve this goal, this US-UK collaborative project brings together expertise in phylogenetics, mathematical modelling, BSL-3 and BSL-4 capabilities, as well as field and clinical expertise in Turkey and Tajikistan with direct access to large collections of human, animal host and vector samples. We will quantify reassortment patterns, bringing together mathematical models with in vitro experiments of selected Bunyaviruses in arthropod and vertebrate cell lines. Statistical inference will allow us to estimate the basic reproduction number for each reassortant and cellular host. At the population level, we will design DNA sequencing and phylodynamic methods to dissect the evolutionary and transmission history of a segmented virus. Thus, our phylogenetic analysis of the field data to be collected in Turkey and Tajikistan will critically evaluate the convolution of point mutations, recombination and reassortment of CCHFV. Phylodynamic methods, adapted and developed in this project, together with field data, will allow us to relate these evolutionary processes to the host switching, temporal and geographical patterns of CCHFV outbreaks. With clinical information and data from Turkey and Tajikistan we will parameterise a mathematical model of CCHFV nosocomial transmission to inform public health decision making. While we focus on the Bunyaviridae family, especially CCHFV, our quantitative methods will be made adjustable to other segmented viruses of great public health relevance.