Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features
Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features
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DOI：
10.1128/jvi.02182-06
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发表时间：
2007-02-01
影响因子：
5.4
通讯作者：
Yuen, Kwok-yung
中科院分区：
文献类型：
--
作者：
Woo, Patrick C. Y.;Wang, Ming;Yuen, Kwok-yung
对三种新型冠状病毒——蝙蝠冠状病毒 HKU4（蝙蝠冠状病毒 HKU4）、蝙蝠冠状病毒 HKU5（假定的 2c 组）和蝙蝠冠状病毒 HKU9（假定的 2d 组）的 12 个完整基因组进行了测序。比较基因组分析表明，三种冠状病毒基因组的各个开放阅读框（ORF）与其他第2组冠状病毒的氨基酸同一性显着高于第1组和第3组冠状病毒。使用胰凝乳蛋白酶样蛋白酶、RNA依赖性RNA聚合酶、解旋酶、刺突和核衣壳构建的系统发育树均表明，第2a组和第2b组以及推定的第2c组和第2d组冠状病毒彼此之间的相关性比第1组和第3组冠状病毒的相关性更密切。还观察到区分这四个亚组的独特基因组特征，包括木瓜蛋白酶样蛋白酶的数量、血凝素酯酶的存在或不存在、膜和核衣壳基因之间的小ORF和ORF（NS7a和NS7b）、核衣壳基因下游的凸出茎环和假结结构、转录调控序列以及包膜基因的核糖体识别信号。这是首次在2型冠状病毒中发现核衣壳基因下游的NS7a和NS7b。蝙蝠冠状病毒 HKU9 中 NS7a 和 NS7b 的高 Ka/Ks 比率意味着这两个 2d 组特异性基因处于高选择压力下，因此正在快速进化。第 2 组冠状病毒的四个亚组可能起源于共同的祖先。对其他国家的蝙蝠以及其他动物中的冠状病毒进行进一步的分子流行病学研究以及完整的基因组测序将有助于更好地了解冠状病毒的多样性及其进化历史。
Twelve complete genomes of three novel coronaviruses-bat coronavirus HKU4 (bat-CoV HKU4), bat-CoV HKU5 (putative group 2c), and bat-CoV HKU9 (putative group 2d)-were sequenced. Comparative genome analysis showed that the various open reading frames (ORFs) of the genomes of the three coronaviruses had significantly higher amino acid identities to those of other group 2 coronaviruses than group 1 and 3 coronaviruses. Phylogenetic trees constructed using chymotrypsin-like protease, RNA-dependent RNA polymerase, helicase, spike, and nucleocapsid all showed that the group 2a and 2b and putative group 2c and 2d coronaviruses are more closely related to each other than to group 1 and 3 coronaviruses. Unique genomic features distinguishing between these four subgroups, including the number of papain-like proteases, the presence or absence of hemagglutinin esterase, small ORFs between the membrane and nucleocapsid genes and ORFs (NS7a and NS7b), bulged stem-loop and pseudoknot structures downstream of the nucleocapsid gene, transcription regulatory sequence, and ribosomal recognition signal for the envelope gene, were also observed. This is the first time that NS7a and NS7b downstream of the nucleocapsid gene has been found in a group 2 coronavirus. The high Ka/Ks ratio of NS7a and NS7b in bat-CoV HKU9 implies that these two group 2d-specific genes are under high selective pressure and hence are rapidly evolving. The four subgroups of group 2 coronaviruses probably originated from a common ancestor. Further molecular epidemiological studies on coronaviruses in the bats of other countries, as well as in other animals, and complete genome sequencing will shed more light on coronavirus diversity and their evolutionary histories.