A comparative phylogenomic analysis of SARS-CoV-2 strains reported from non-human mammalian species and environmental samples.
A comparative phylogenomic analysis of SARS-CoV-2 strains reported from non-human mammalian species and environmental samples.
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DOI：
10.1007/s11033-020-05879-5
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发表时间：
2020-11
影响因子：
2.8
通讯作者：
Shabbir MZ
中科院分区：
文献类型：
--
作者：
Ul-Rahman A;Shabbir MAB;Aziz MW;Yaqub S;Mehmood A;Raza MA;Shabbir MZ
冠状病毒（Coronaviruses，CoV）感染广泛的家养和野生哺乳动物。这些病毒具有跨物种屏障和感染人类的潜力和趋势。新型人类冠状病毒2019-nCoV（hCoV-19）出现在中国武汉，并引起了全球大流行。SARS-CoV-2的基因组特征可能将种间传播和适应归因于新的宿主，因此必须阐明病毒基因组的进化动力学及其差异宿主选择的倾向。我们对SARS-CoV-2毒株（n = 39）的所有编码基因序列进行了计算机分析，这些毒株来源于一系列非人类哺乳动物物种，包括穿山甲、蝙蝠、狗、猫、老虎、水貂、小鼠，以及环境样品，如废水、空气和门把手和海鲜市场的表面样品。与SARS-CoV-2参考株（MN 908947;武汉-胡-1）相比，系统发育和比较残基分析揭示了三种变体的循环，包括来自人类的hCoV-19病毒和来自蝙蝠和穿山甲的两种hCoV-19相关前体。犬、猫、虎、貂、小鼠、蝙蝠和穿山甲来源的SARS-CoV-2序列之间缺乏明显的差异以及最大的遗传同源性，表明这些毒株可能从共同的祖先进化而来。在刺突蛋白的受体结合结构域（RBD）中观察到几个残基取代，从而得出结论，该病毒对宿主物种具有混杂性，其中可能需要基因组改变以适应新的宿主。然而，这种推测需要在体外调查，以释放的影响，对物种跳跃和疾病的发病机制的取代。本文的在线版本（10.1007/s11033-020-05879-5）包含补充材料，可供授权用户使用。
Coronaviruses (CoVs) infect a wide range of domestic and wild mammals. These viruses have a potential and tendency to cross-species barriers and infect humans. Novel human coronavirus 2019-nCoV (hCoV-19) emerged from Wuhan, China, and has caused a global pandemic. Genomic features of SARS-CoV-2 may attribute inter-species transmission and adaptation to a novel host, and therefore is imperative to explicate the evolutionary dynamics of the viral genome and its propensity for differential host selection. We conducted an in silico analysis of all the coding gene sequences of SARS-CoV-2 strains (n = 39) originating from a range of non-human mammalian species, including pangolin, bat, dog, cat, tiger, mink, mouse, and the environmental samples such as wastewater, air and surface samples from the door handle and seafood market. Compared to the reference SARS-CoV-2 strain (MN908947; Wuhan-Hu-1), phylogenetic and comparative residue analysis revealed the circulation of three variants, including hCoV-19 virus from humans and two hCoV-19-related precursors from bats and pangolins. A lack of obvious differences as well as a maximum genetic homology among dog-, cat-, tiger-, mink-, mouse-, bat- and pangolin-derived SARS-CoV-2 sequences suggested a likely evolution of these strains from a common ancestor. Several residue substitutions were observed in the receptor-binding domain (RBD) of the spike protein, concluding a promiscuous nature of the virus for host species where genomic alternations may be required for the adaptation to novel host/s. However, such speculation needs in vitro investigations to unleash the influence of substitutions towards species-jump and disease pathogenesis. The online version of this article (10.1007/s11033-020-05879-5) contains supplementary material, which is available to authorized users.
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DOI：
10.1016/s0140-6736(03)14121-9
发表时间：
2003-08-16
期刊：
Lancet (London, England)
影响因子：
--
作者：
Ng SK
通讯作者：
Ng SK
DOI：
10.1038/nrmicro.2016.81
发表时间：
2016-08
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
de Wit E;van Doremalen N;Falzarano D;Munster VJ
通讯作者：
Munster VJ
影响因子：
2.5
作者：
To, Kelvin K. W.;Hung, Ivan F. N.;Yuen, Kwok-Yung
通讯作者：
Yuen, Kwok-Yung
影响因子：
5.4
作者：
Sheahan, Timothy;Rockx, Barry;Baric, Ralph
通讯作者：
Baric, Ralph
影响因子：
12.7
作者：
Li, Xingguang;Zai, Junjie;Chaillon, Antoine
通讯作者：
Chaillon, Antoine