基于RNA条形码技术对新型冠状病毒的鉴定

Identification of SARS-CoV-2 based on RNA barcoding

旨在设计一种通过RNA条形码片段对SARS-CoV-2进行更快、更准确鉴定的技术。该技术基于NCBI数据库对所有Beta-CoV属以及7种HCoVs的序列进行筛选并构建序列库。通过生物信息学方法对序列库进行遗传多样性分析、遗传距离分析以及系统发育树的构建,从而测试条形码片段在不同情况下对鉴定SARS-CoV-2的准确性与稳定性。基于SNP位点对序列进行剪裁并利用NCBI的Blast功能将剪裁的片段进行打分,得到鉴别效果最优的条形码片段并可视化。结果表明,RNA条形码片段可以准确地将SARS-CoV-2从序列库内包含的所有毒株中鉴定出来,而通过Blast打分以及P值检验最终得到的2条条形码片段(分别位于ORF1ab和S基因编码区)对鉴定SARS-CoV-2具有很好的稳定性。RNA条形码技术不仅有利于探索SARS-CoV-2全基因组序列多态性与物种特异性遗传标记的关系,还有利于为SARS-CoV-2的鉴定技术提供新思路。

It aimed to design a technology for the faster and more accurate identification of SARS-CoV-2 through RNA barcode segments.Sequences of Beta-CoV genera and 7 HCoVs were screened to construct the sequences database based on the NCBI online database.The genetic diversity analysis,genetic distance analysis and phylogenetic tree construction of the sequences database were performed on bioinformatics methods,so as to examine the accuracy and stability of barcode segments in identifying SARS-CoV-2 in different cases.Finally,the fragments clipped from the SNP sites on sequences were scored by using the Blast on NCBI to obtain the barcode segments and visual barcodes with the optimal identification effect.Above results showed that the RNA barcode segments could precisely identify SARS-CoV-2 from all strains within the sequences database,and the two barcode segments(located in the coding regions of ORF1ab gene and S gene respectively)screened with Blast Total scores and P value tests also had good stability for identifying SARS-CoV-2.RNA barcoding contributed to explore the relationship between the whole genome sequence polymorphism of SARS-CoV-2 and the species-specific genetic markers and to provide new idea for identification technologies of SARS-CoV-2.