Phylogenetic and experimental reconstruction of zoonotic transmission of human coronaviruses

自2002/2003年SARS冠状病毒在中国出现以来，冠状病毒受到了相当大的关注。SARS冠状病毒感染人类的例子表明，冠状病毒可以跨越物种屏障，从动物宿主到人类，并在人类中引起严重和致命的疾病。2012年MERS-CoV的出现表明，冠状病毒的人畜共患传播并非罕见事件。这两种病毒在蝙蝠中都有近亲，此外，中间宿主，如浣熊狗、果子狸（SARS冠状病毒）和单峰骆驼（MERS冠状病毒）已被提议促进人畜共患传播。单峰骆驼携带MERS CoV，可能是蝙蝠和人类之间的桥梁水库，这一发现为病毒出现的生态学提供了一个重要的范例。有趣的是，人类冠状病毒229 E（HCoV-229 E;导致人类普通感冒）似乎具有类似的人畜共患病传播史，因为在蝙蝠和骆驼科物种（羊驼和单峰骆驼）中检测到近亲。虽然MERS冠状病毒的人畜共患传播的历史非常近，从人类和骆驼分离的病毒之间的差异相当小，骆驼-229 E样冠状病毒和HCoV-229 E已经有很大的分歧，拟议项目的目的是确定和表征关键物种的障碍，冠状病毒人畜共患传播使用HCoV-229 E系统作为一个模型。我们将分析在病毒进入步骤（钉受体相互作用）和细胞内复制过程中的物种障碍。重要的是，我们的研究涉及蝙蝠-骆驼-和人229 E病毒及其真实宿主的原代气道上皮培养物，使我们能够模拟上呼吸道的跨物种感染。具体而言，我们会集中于：（a） 跨物种传播的宿主决定因素，即先天免疫应答（I型干扰素系统），我们将评估非编码RNA（长非编码RNA和微RNA）是否可能构成关键物种屏障，以及（B） 通过跟踪病毒对新宿主的适应，以及鉴定适应过程中最不稳定的基因组区域/病毒结构域，确定跨物种传播的病毒决定因素。相关性：蝙蝠已被证明携带各种不同的冠状病毒物种，包括人类冠状病毒的近亲（HCoV-229 E，SARS-CoV，MERS-CoV）。因此，确定影响跨种属传播的关键病毒-宿主相互作用非常重要。几个全长蝙蝠-229E-样冠状病毒基因组序列的可用性，骆驼-229E-样冠状病毒的发现，以及来自真实宿主的原代上皮靶细胞的可用性，为研究冠状病毒的人畜共患病传播的关键物种障碍提供了前所未有的机会。这些信息对于评估未来可能的人畜共患病传播的风险和提供有效的抗病毒干预的概念框架是非常有价值的。

Coronaviruses have received considerable attention since the emergence of SARS-CoV in China 2002/2003. SARS-CoV infection in people exemplified that coronaviruses can cross the species barrier from an animal reservoir to humans and cause severe and lethal disease in humans. Theemergence of MERS-CoV in 2012 showed that zoonotic transmission of coronaviruses is not a rare event. Both viruses have close relatives in bats, and moreover, intermediate hosts, such asracoon dogs, civet cats (SARS-CoV) and dromedary camels (MERS-CoV) have been proposed to facilitate zoonotic transmission. The discovery that dromedary camels harbour MERS-CoV and may act as a bridge reservoir between bats and humans provides an important paradigm for the ecology of viral emergence. Interestingly, the human coronavirus 229E (HCoV-229E; causing common cold in humans), appears to have a similar history of zoonotic transmission, since close relatives were detected in bats as well as in camelid species (alpacas and dromedary camels). While MERS-CoV has a very recent history of zoonotic transmission and differences between viruses isolated from humans and camels are rather small, camel-229E-like-CoV and HCoV-229E have already diverged considerably.The aim of the proposed project is to identify and characterize critical species barriers of CoV zoonotic transmission by using the HCoV-229E system as a model. We will analyse species barriers at the virus entry step (spike-receptor interaction) and during intracellular replication. Importantly, our studies involve bat- camel- and human 229E viruses and primary airway epithelial cultures of their authentic hosts, allowing us to mimic cross-species infection of the upper airways. Specifically, we will focus on:(a) host determinants of cross species transmission, namely innate immune responses (type I interferon system), and we will assess if non-coding RNAs (long non-coding RNA and micro-RNAs) may constitute a critical species barrier, and(b) virus determinants of cross species transmission by following virus adaptation to a new host, and identification of genomic regions/viral domains that are most volatile during adaptation. Relevance: Bats have been shown to harbour a wide variety of diverse CoV species, including close relatives of human coronaviruses (HCoV-229E, SARS-CoV, MERS-CoV). Therefore it is important to define critical virus-host interactions that impact on cross-species transmission. The availability of several full-length bat-229E-like-CoV genome sequences, the discovery of a camel-229E-like-CoV, and the availability of primary epithelial target cells from the authentic hosts offers an unprecedented opportunity to study critical species barriers for the zoonotic transmission of CoVs. This information is extremely valuable to assess the risk of possible future zoonotic transmissions and provide a conceptional framework for efficacious antiviral intervention.