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Discovering genomic patterns in SARS-CoV-2 variants
International Journal of Intelligent Systems ( IF 7 ) Pub Date : 2020-07-24 , DOI: 10.1002/int.22268
Gianni D'Angelo 1 , Francesco Palmieri 1
Affiliation  

SARS‐CoV‐2 is a novel severe acute respiratory syndrome‐like coronavirus (SARS‐CoV), which is responsible of the ongoing world pandemic of COVID‐19 disease. Although many approaches are being investigated to address this issue, nowaday there are no vaccines available and there is little evidence supporting the efficiency of potential therapeutic agents. Moreover, the high mutation rate of this virus heavily affects the understanding of its evolution and diffusion mechanisms, and, in turn, the development of effective solutions. In this study, two novel algorithms are provided for finding out recurrent patterns of nucleotide subsequences of different SARS‐CoV‐2 genomes as a unique signature capable of identifying the most peculiar features of the pathogen. In particular, we provide several subsequence patterns related to the Spike glycoprotein, which is believed to be the main target for developing effective drugs and vaccines against the COVID‐19 disease because of its role in the entrance of coronaviruses into host cells. The experimental results, obtained by analyzing 5000 genomes of SARS‐CoV‐2, have shown that the extracted patterns are able to recognize the Spyke protein in the 99.35% of the considered genomes. In addition, such patterns have proven to be highly discriminating with respect to other pathogenic genomes, such as SARS, Middle East respiratory syndrome, Nipah, and the streptococcus bacteria. We hope that the findings presented in this study can help specialists in speeding up the design of more accurate drugs or vaccines against SARS‐CoV‐2.

中文翻译:

发现 SARS-CoV-2 变体中的基因组模式

SARS-CoV-2 是一种新型的严重急性呼吸系统综合症样冠状病毒 (SARS-CoV),它导致了 COVID-19 疾病的持续全球大流行。尽管正在研究许多方法来解决这个问题,但目前还没有可用的疫苗,而且几乎没有证据支持潜在治疗剂的有效性。此外,该病毒的高突变率严重影响对其进化和传播机制的理解,进而影响有效解决方案的开发。在这项研究中,提供了两种新算法来找出不同 SARS-CoV-2 基因组的核苷酸亚序列的重复模式,作为能够识别病原体最奇特特征的独特特征。特别是,我们提供了几种与 Spike 糖蛋白相关的子序列模式,由于其在冠状病毒进入宿主细胞中的作用,它被认为是开发针对 COVID-19 疾病的有效药物和疫苗的主要目标。通过分析 5000 个 SARS-CoV-2 基因组获得的实验结果表明,提取的模式能够识别 99.35% 所考虑基因组中的 Spyke 蛋白。此外,这些模式已被证明对其他致病基因组具有高度辨别力,例如 SARS、中东呼吸综合征、尼帕和链球菌。我们希望这项研究中的发现可以帮助专家加快设计更准确的抗 SARS-CoV-2 药物或疫苗。
更新日期:2020-07-24
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