基于全基因组序列的新型冠状病毒SARS-CoV-2多算法进化树分析

Analyses of SARS-CoV-2 with Multi-Algorithm Phylogenetic Trees Based on Whole Genome Sequences

新型冠状病毒(SARS-CoV-2)作为一种RNA病毒,具有高突变率的特征,自新型冠状病毒肺炎(COVID-19)发生以来,病毒基因组已出现了一定程度的突变,可以通过进化分析对其进行分类,以辅助分析病毒感染源。由于时间较短,总体突变率仍然较低,利用单一算法构建的进化树结构可靠性不高。本文用Paup、MrBayes和MEGA软件,通过不同算法构建进化树,对目前GenBank中所有的SARS-CoV-2基因组进行了分析。不同算法所得到的多个进化树中,部分序列分支结构相同或相似,且相应的病毒宿主间可能存在交集,通过比较分析多个树之间的相似结构,可为病毒的来源提供参考信息。随着病毒的进化和基因组数据库的不断积累,预计利用多算法构建进化树去筛选相同分枝结构的方法的有效性将逐步提升,可作为感染源分析的参考方法之一。

SARS-CoV-2 is an RNA virus,and has a high mutation rate.The outbreak of coronavirus disease2019(COVID-19)began in Wuhan,Hubei Province,China in December 2019.Since then,a certain number of mutations have occurred in the SARS-CoV-2 genome.These mutations can be classified by phylogenetic analyses to help find the infection source.However,the overall mutation rate is low,and the structure of a phylogenetic tree constructed by a single algorithm is not sufficiently reliable.To improve the reliability of classification,Paup,MrBayes,and MEGA were used to construct phylogenetic trees by different algorithms to analyze the genomes of all SARS-CoV-2 viruses in GenBank.In all phylogenetic trees,some sequences were clustered together in a similar pattern that coincided with the intersection of virus hosts.By comparing and analyzing similar structures between multiple phylogenetic trees,some information about the infection source was revealed.As SARS-CoV-2 evolves and genomic databases become enriched,the method of screening will provide increasingly useful information about infection sources and pathways.