MOLECULAR BARRIERS TO THE EMERGENCE OF CORONAVIRUSES IN HUMANS

上下文。新病毒的出现威胁着人类的健康和繁荣。这些“新”病毒的主要来源是现有动物病毒对人类种群的“溢出”。新冠肺炎大流行就是这种情况，一种新的冠状病毒(SARS-CoV-2)从马蹄蝠传播给人类(可能是通过中间动物物种)。其他冠状病毒(CoV)溢出事件包括SARS和MERS，有证据表明CoV可能特别擅长在物种之间跳跃。如果要预防未来的冠状病毒大流行，迫切需要更好地预测哪些动物冠状病毒可能出现在人类种群中，并确定允许或阻止这种传播的因素。病毒从动物传播到人类存在多重障碍。人类必须与动物宿主接触，病毒还必须能够与完成病毒生命周期所需的分子的“人类版本”相互作用。例如，SARS-CoV-2的病毒刺突蛋白与宿主受体蛋白ACE2相互作用(以入侵人类细胞)。然而，SARS-CoV-2刺突蛋白不能使用小鼠版本的ACE2，这有效地形成了一种屏障，保护小鼠免受SARS-CoV-2感染。作为进一步的屏障，人类和动物细胞包含了一系列可以阻止病毒的防御系统。病毒必须进化以克服其正常宿主物种中的这些抗病毒防御，但这些策略可能在新的宿主物种中无效。因此，我们细胞内的抗病毒防御可以形成一个重要的障碍，必须克服这个障碍才能使病毒出现在人类群体中。通过对多种病毒的研究，已经确定了许多这样的抗病毒防御措施，这些防御措施通常是由干扰素刺激的，干扰素是细胞对病毒感染做出反应时释放的蛋白质。因此，通过检查干扰素刺激基因(ISGs)，可以发现未知的抗病毒防御机制。我们提议的工作将确定可能限制冠状病毒出现的抗病毒ISG防御。此外，由于干扰素的反应可以在很大程度上影响冠状病毒诱导的疾病的严重程度，提高我们对干扰素和ISGs对冠状病毒的影响的理解可以为新冠肺炎的发病机制提供帮助。我们将通过使用人工智能/机器学习来搜索目前在蝙蝠体内传播的CoV的基因组序列模式，从而识别最有可能在人类中出现的CoV。由于大多数现有的人类冠状病毒起源于蝙蝠，而蝙蝠携带其他病毒，如SARS-CoV-2，这将有助于我们准确定位具有人类大流行潜力的特定冠状病毒。为了识别影响冠状病毒的抗病毒ISG防御措施，我们将进行筛查，系统地测量&gt；1000个独立ISG抑制特定的高风险BAT冠状病毒(被认为使用机器学习)、人类SARS冠状病毒或人类季节性冠状病毒的能力。这种方法将揭示针对冠状病毒的ISG防御。为了揭示这些因素中的哪些因素可能阻止/允许特定蝙蝠冠状病毒的出现，我们将比较马蹄蝠(储存物种)、人类和一组可能的中间物种对冠状病毒出现的屏障的同等抗病毒ISG防御的能力。应用和益处。在这个项目中，我们将阐明冠状病毒生物学的一个重要领域，就病毒出现的风险进行有效的沟通，培训下一代病毒学家，并促进该领域的进一步研究。从长远来看，我们的研究确定了冠状病毒出现的分子细节，将有助于识别具有更大流行潜力的冠状病毒，改善全球监测工作。此外，干扰素在冠状病毒发病机制中扮演的关键角色意味着这项研究可能会揭示SARS-CoV-2疾病的结果。

Context. The emergence of new viruses threatens human health and prosperity. The main source of these 'new' viruses is the 'spillover' of existing animal viruses into human populations. This is the case with the COVID-19 pandemic, where a 'new' coronavirus (SARS-CoV-2) was transmitted from horseshoe bats to humans (possibly via an intermediate animal species). Other coronavirus (CoV) spillover events include SARS and MERS, and evidence suggests CoVs may be particularly adept at jumping between species. If future CoV pandemics are to be prevented, there is an urgent need to better predict which animal CoVs are poised to emerge in human populations, and to identify the factors that permit or prevent such transmission.There are multiple barriers to the transmission of viruses from animals to humans. Humans must have contact with the animal reservoir, and the virus must also be able to interact with 'human versions' of the molecules needed to complete the viral lifecycle. For example, the viral spike protein of SARS-CoV-2 interacts with the host receptor protein ACE2 (in order to invade human cells). However, the SARS-CoV-2 spike protein cannot use the mouse version of ACE2, and this effectively forms a barrier that protects mice from SARS-CoV-2 infection. As a further barrier, human and animal cells contain an arsenal of defences that can block viruses. Viruses must evolve to overcome these antiviral defences in their normal host species, but these strategies may not be effective in a new host species. Thus, the antiviral defences within our cells can form an important barrier that must be overcome in order for viruses to emerge in human populations. Through the study of diverse viruses, many such antiviral defences have been identified, and these defences are often stimulated by interferons, which are proteins released by cells in response to viral infection. Thus, by examining interferon-stimulated genes (ISGs), unidentified antiviral defences can be found. Our proposed work will identify antiviral ISG defences that might constrain CoV emergence. Moreover, as interferon responses can heavily influence the severity of coronavirus-induced disease, improving our understanding of the effect of interferons and ISGs on CoVs could shed light on COVID-19 pathogenesis.Aims. We will identify CoVs most likely to emerge in humans by using artificial intelligence/machine learning to search for patterns in the genome sequences of CoVs currently circulating in bats. As most existing human CoVs have origins in bats, and bats harbour other viruses like SARS-CoV-2, this will help us pinpoint specific CoVs with human pandemic potential.To identify the antiviral ISG defences impacting CoVs, we will carry out screens to systematically measure the ability of >1000 individual ISGs to inhibit either the specific 'high risk' bat CoVs (deemed using machine learning), the human SARS CoVs, or human seasonal CoVs. This approach will reveal the ISG defences that target coronaviruses. To uncover which of these factors might prevent/permit the emergence of specific bat CoVs, we will compare the abilities of the equivalent antiviral ISG defences from horseshoe bats (the reservoir species), humans and a panel of possible intermediate species, to act as a barrier to coronavirus emergence in humans.Applications and benefits. During this project we will illuminate an important area of coronavirus biology, communicate effectively about the risks of virus emergence, train the next generation of virologists and stimulate further research in this field. In the longer term, our research defining the molecular details of coronavirus emergence will help identify coronaviruses with increased pandemic potential, improving global surveillance efforts. In addition, the pivotal role that interferons play in coronavirus pathogenesis means this research could potentially shed light on SARS-CoV-2 disease outcomes.