Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
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DOI：
10.1080/22221751.2020.1719902
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发表时间：
2020-01-01
影响因子：
13.2
通讯作者：
Yuen, Kwok-Yung
中科院分区：
文献类型：
--
作者：
Chan, Jasper Fuk-Woo;Kok, Kin-Hang;Yuen, Kwok-Yung
2019年底神秘爆发的非典型肺炎追溯到中国武汉的一个海鲜批发市场。几周内，世界卫生组织公布了一种暂时命名为2019新型冠状病毒（2019-nCoV）的新型冠状病毒。我们对来自2019-nCoV感染患者的病毒基因组进行了生物信息学分析，并将其与其他相关冠状病毒基因组进行了比较。总体而言，2019-nCoV的基因组与蝙蝠SARS-like-CoVZXC 21的核苷酸同源性为89%，与人类SARS-CoV的核苷酸同源性为82%。其orf 1 a/B、刺突蛋白、囊膜蛋白、核蛋白的系统发育树与蝙蝠、果子狸和人SARS冠状病毒的系统发育树也很接近。然而，2019-nCoV的Spike受体结合结构域的外部子结构域与其他SARS相关冠状病毒只有40%的氨基酸同一性。值得注意的是，它的orf3b编码一种全新的短蛋白。此外，它的新orf8可能编码一种分泌蛋白，具有一个α螺旋，随后是一个含有六条链的β折叠。从果子狸在SARS中的作用和骆驼在MERS中的作用中学习，寻找2019-nCoV及其更古老的病毒的动物来源对于了解这种新型谱系B β冠状病毒的起源和进化至关重要。这些发现为进一步研究其发病机制提供了基础，并为这种新出现的感染提供了诊断，抗病毒和疫苗接种策略的优化设计。
A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike's receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.