新型冠状病毒基因组序列的网络平台与基因分型

新型冠状病毒(SARS-CoV-2)是引起2019新型冠状病毒肺炎(COVID-19)的病原体,目前COVID-19仍在世界范围内大规模流行。随着学者对SARS-CoV-2研究的不断深入,以及各大数据库的序列资源共享,一些学者开发了SARS-CoV-2相关序列分析网络在线平台,并发表了对SARS-CoV-2基因分型、命名的规则。"GISAID"是目前SARS-CoV-2基因组序列共享和储存最大的数据库,"Nextstrain"和"CoV-GLUE"是国际最常用的SARS-CoV-2序列分析平台。目前有四种比较通用的SARS-CoV-2的基因分型方法,在本文中分别简称为:"中国分型法"、"Pangolin分型法"、"GISAID分型法"和"Nextstrain分型法"。这四种分型方法的定义不尽相同,但又有相似之处。本综述对目前SARS-CoV-2在线分析网络平台和不同的基因分型方法进行了较为系统的介绍、对比和总结。

Genomic Analysis Platforms and Typing Methods for SARS-CoV-2 Genome Sequences

SARS-CoV-2 is the pathogen that causes coronavirus disease 2019(COVID-19).COVID-19 is still a worldwide pandemic.With the continuous in-depth study of SARS-CoV-2 and the sharing of the sequence resources in major databases,some scholars have developed online platforms for the analysis of SARS-CoV-2 genome sequences.Also,many studies have proposed SARS-CoV-2 genomic typing methods."GISAID"is currently the largest database for sharing and storing SARS-CoV-2 genome sequences."Nextstrain"and"CoVGlue"are the most noted SARS-CoV-2 sequence analysis platforms.Currently,four SARS-CoV-2 phylogenetic typing methods are commonly used,which,in this review,are referred to as the"Chinese lineage typing method",the"Pangolin lineage typing method",the"GISAID clade typing method",and the"Nextstrain cluster typing method".The bases of these methods are not the same,but there are similarities.This review provides a comprehensive introduction,comparison,and summary of the online analysis platforms of SARS-CoV-2 and the different genomic typing methods.