新型冠状病毒刺突糖蛋白D614G变异的时间变化和空间分布特征分析

Spatial and temporal distribution characteristics of SARS-CoV-2 with D614G mutation in spike protein

目的通过对新型冠状病毒公共数据库的序列进行分析,了解刺突糖蛋白(S蛋白)D614G变异时间变化和空间分布特征。方法本研究纳入截止至2020年7月21日在国内外新型冠状病毒公共数据库(GenBank、EpiCoV、CNGBdb、Genome Warehouse和NMDC)公布的核酸序列,对各数据库获取的序列进行去重、序列过滤和比对等数据分析以确定纳入序列的S蛋白D614G变异情况,并对包含该变异的毒株进行时间变化和空间分布特征分析。结果本研究经数据过滤后最终纳入分析的序列56201条,其中来自中国的序列1060条(1.9%),其他国家来源的序列55141条(98.1%),13570条(24.1%)序列为野生型,42631条(75.9%)序列发生D614G变异。D614G变异最早在四川(EpiCoV数据库:EPI_ISL_451345)和浙江(NMDC数据库:NMDC60013101-01)2020年1月24日采集样本并测序的毒株中被发现,该2株毒株均与来自武汉(2019年12月30日)的毒株参考序列(NC_045512)同源性最高,同源性均为99.9%以上。在纳入分析不同时间的序列中,D614G变异毒株的构成比呈明显上升趋势,自2020年2月份起至2020年6月份,D614G构成比均明显高于2019年12月份的数据,均P<0.05,D614G变异构成比最多的国家为比利时(86.7%),其次为英国(79.0%)和美国(76.1%),构成比最少的国家为中国(20.2%)。在来自中国毒株的序列中,D614G变异也呈上升趋势,自2020年3月份起至2020年6月份,D614G构成比均明显高于2019年12月份的数据,均P<0.05。国内曾发现D614G变异毒株主要分布在广州(50.9%)、台湾(27.1%)和北京(10.8%)。结论新型冠状病毒S蛋白D614G变异毒株构成比呈现明显上升趋势,且主要存在于国外的毒株,应对其动态监测,进一步了解其流行病学特点。

Objective To understand the spatial and temporal distribution characteristics of severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)with D614G mutation in spike protein by analyzing the SARS-CoV-2 sequences from public databases.Methods Up to July 21,2020,sequences archived in five SARS-CoV-2 public databases,including GenBank,EpiCoV,CNGBdb,Genome Warehouse,and NMDC,were acquired;and bioinformatics analysis methods(deleting the repeat sequences in the five databases,filtering the low quality sequences,and identifying the mutation by multiple sequences alignment)were used to analyze the sequences'mutation,and analyzed the spatial and temporal distribution characteristics of SARS-CoV-2 with D614G mutation in spike protein.Results In this study,56201 SARS-CoV-2 sequences were enrolled,including 1060 sequences(1.9%)from China and 55141(98.1%)from other countries.Among these data,13570 viral strains(24.1%)were wild type and 42631 sequences(75.9%)had D614G mutation.The earliest viral stains harbored D614G mutation were found in Sichuan(EpiCoV database:EPI_ISL_451345)and Zhejiang provinces(NMDC database:NMDC60013101-01),collected on January 24,2020;the similarities of these sequences were more than 99.9%as compared to the reference sequence from Wuhan city(2019-12-24;NC_0455123)which archived in GenBank database.The results of temporal distribution analysis showed that the ratios of SARS-CoV-2 with D614G mutation increased from December,2019 to June,2020 worldwide,and the ratios have significantly increased since February,2020(all P<0.05).The results of spatial distribution analysis showed SARS-CoV-2 with D614G mutation were most frequently found in Belgium(86.7%),the United Kingdom(79.0%),and the United States(76.1%);however,only 20.2%viral strains from China harbored this mutation.In addition,the 1060 SARS-CoV-2 sequences from China were also analyzed,and the results also revealed that the ratios of SARS-CoV-2 with D614G mutation have increased since the epidemic outbreak,especially since March,2020(all P<0.05);and D614G mutation was most frequently found in Guangzhou(50.9%),Taiwan(27.1%),and Beijing(10.8%).Conclusion This study revealed the ratios of SARS-CoV-2 with D614G mutation have increased since the epidemic outbreak,and the distributions of viral strains with D614G mutation are mainly in foreign countries.Further researches are needed to understand the dynamic change of the viral strains with this mutation.