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

基因组分割对病毒基因表达控制和RNA组装成新生病毒粒子具有重要意义。它还创造了重组的可能性：在共同感染同一细胞的病毒之间交换完整的基因片段。重配在数量上不同于分子内重组，因为它允许从单个共感染细胞中出现许多不同的基因型。分割不仅增强了遗传多样性，而且由于在群体规模上重组成功的罕见情况，它在许多分段病毒的进化史中起着独特的作用。通过重新组合从布尼亚病毒中产生新病毒的一个显著例子是阿里病毒。流感（IAV）是最具特征的分节病毒，重组促进了1957年、1968年和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7种易流行疾病中，有3种是布尼亚病毒。因此，本项目的首要假设是，片段病毒的重组不仅在推动其多样化和进化方面起着重要作用，而且还极大地改变了它们的生态和传播动态。具体来说，我们的目标是1)建立一个分节病毒家族的细胞内生命周期的数学模型，并结合体外实验首次量化它们的病毒复制动力学和重排频率；2)制定标准化的测序方案，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）重排的进化和流行病学意义。该项目将建立一个生物库，收集来自土耳其和塔吉克斯坦疫区的临床和现场样本。将利用临床和现场数据，使我们的方法和结果有可能为控制战略提供信息并预测疫情风险。本项目开发的定量方法将有助于Sorvillo等人为CCHFV倡导的“同一个健康”方法。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节布尼亚病毒的重配频率和适应性。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、动物宿主和媒介样本。我们将量化重组模式，将数学模型与节肢动物和脊椎动物细胞系中选定的布尼亚病毒的体外实验结合起来。统计推断将使我们能够估计每个重组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分段病毒的进化和传播历史。因此，我们将对在土耳其和塔吉克斯坦收集的现场数据进行系统发育分析，以批判性地评估CCHFV的点突变、重组和重配的卷积。本项目采用和发展的系统动力学方法，加上实地数据，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，我们将参数化CCHFV医院传播的数学模型，为公共卫生决策提供信息。虽然我们的重点是布尼亚病毒科，特别是CCHFV，但我们的定量方法将调整到与公共卫生有重大关系的其他分节病毒。

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.