The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet little is known of the intrinsic organization and evolution of the genome. To this end, we present a mathematical method for the genomic spectrum, a kind of barcode, of SARS-CoV-2 and common human coronaviruses. The genomic spectrum is constructed according to the periodic distributions of nucleotides, and therefore reflects the unique characteristics of the genome. The results demonstrate that coronavirus SARS-CoV-2 exhibits dinucleotide TT islands in the non-structural proteins 3, 4, 5, and 6. Further analysis of the dinucleotide regions suggests that the dinucleotide repeats are increased during evolution and may confer the evolutionary fitness of the virus. The special dinucleotide regions in the SARS-CoV-2 genome identified in this study may become diagnostic and pharmaceutical targets in monitoring and curing the COVID-19 disease.
Analysis of pangolin metagenomic datasets reveals significant contamination, raising concerns for pangolin CoV host attribution
来自穿山甲组织标本的宏基因组数据集先前已经产生了SARS相关冠状病毒，其受体结合结构域与SARS-CoV-2具有高度同源性，表明人类病毒的这一特征可能通过重组而存在潜在的人畜共患来源（Liu et al. 2019，Lam et al. 2020，Xiao et al. 2020，Liu et al. 2020）。在这里，我们重新审视这些已发布的数据集。我们报告说，只有少数穿山甲样品被发现含有冠状病毒读段，即使在低丰度，而其他非穿山甲宿主病毒以更高的丰度存在。我们还发现了人类、啮齿动物和其他哺乳动物基因序列的广泛污染，这是一个令人惊讶的发现。此外，我们还发现了许多嵌在标准实验室克隆载体中的穿山甲CoV序列，这表明穿山甲标本可能被来自合成生物学实验的序列污染。最后，我们发现了第三个穿山甲数据集（He et al. 2022），其中SARSr-CoV序列水平较低，并且几个穿山甲样品受到了明确的广泛污染。由于这些原因，我们发现有问题的穿山甲在活着的时候不太可能感染冠状病毒，并且所有引用的论文的当前版本都声称穿山甲感染了SARS-r CoV的人畜共患病，需要进行大量的更正，并且应该撤回，直到做出这样的更正。
Combining detection and reconstruction of correlational and quasi-periodic motifs in viral genomic sequences with transitional genome mapping: Application to COVID-19
基因组自身的过渡自同构映射（Transitional Automorphic Mapping of the Genome on Itself，TAMGI）方法旨在结合病毒基因组RNA/DNA序列中相关和准周期模体的检测和重建。通过TAMGI重建的基序对于插入缺失和点突变是稳健的，并且可以尝试作为推定的治疗靶标。我们开发并测试了相关的理论和统计标准的TAMGI应用程序。TAMGI的应用通过研究包装在类似病毒的螺旋衣壳中的严重急性呼吸道综合征冠状病毒SARS-CoV和SARS-CoV-2（后者的冠状病毒SARS-CoV-2负责COVID-19大流行）的基因组中的基序来说明。这样的核糖核衣壳被转运到球形膜被膜与掺入刺突糖蛋白。另外两个例子涉及二十面体衣壳病毒的基因组，卫星烟草花叶病毒（STMV）和噬菌体PHIX 174。这些病毒基因组中的部分准周期基序是由于基因组ssRNA/ssDNA与核衣壳蛋白之间的弱特异性合作相互作用而进化的。衣壳的对称性导致相关基因组序列中特定准周期基序的自然选择。一般来说，TAMGI为研究许多分子机制提供了一个方便的工具，这些机制涉及准周期基序和完整重复序列、基因组组织、顺式/反式调节元件的背景分析、数据挖掘以及基因组序列中的相关性。
Distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein: a potential hint at the possibility of local iron dysregulation in COVID-19
