2021年海南省2例轻型新冠肺炎病例相关新冠病毒德尔塔变异株的分子特征分析

Molecular Epidemiological Characteristics of the Delta Variant of SARS-CoV-2 from Two Mild Cases in 2021 in Hainan Province,China

本文对2021年海南省2例感染引起本土轻型新冠肺炎病例的新冠病毒进行全基因组测定和序列分析,研究该病毒的分子特征和分子进化规律。通过荧光定量RT-PCR法检测ORF1ab和N靶基因,应用Illumina公司的MiSeq深度测序平台进行全基因组序列测定,使用MEGA 10.1.8和DNASTAR 7.0.1生物信息学软件进行多序列比对和分析,并采用邻位归并法(Neighbour-joining)绘制系统进化树。2例新冠病毒(HN0801和HN0802)均属于德尔塔变异株,与武汉参考序列(NC_045512)基因序列相似性分别为99.7%和99.8%,系统进化树显示它们位于同一进化分支(B.1.617.2)的不同簇上,共有45个核苷酸突变位点,引起38个氨基酸位点改变,其中34个错义突变、6个同义突变、4个氨基酸位点缺失;刺突(S)糖蛋白发现B.1.617.2谱系共同突变特征L452R、T478K,以及T19R、G142D、D614G、P681R、D950N、R158G关键变异位点。HN0801同2021年7月江苏省南京市代表株基因序列100%相似,而HN0802与南京市疫情代表株基因组相似性较低。结合流行病学调查和基因组序列分析,这2例新冠病毒均属于新冠病毒德尔塔变异株,2例确诊病例之间没有明确的流行病学关联,为两条不同的传播链引起的相互独立的散发病例。本研究为海南省新冠病毒变异株的监测和新冠疫情防控提供了基础数据。

Two severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)strains(HN0801 and HN0802)from two patients with coronavirus disease 2019(COVID-19)in Hainan Province(China)in 2021were studied.The complete genome of HN0801 and HN0802 was sequenced.Then,the molecular characteristics and molecular evolutionary rules of SARS-CoV-2 in Hainan Province were studied.ORF1ab and N target genes were detected by fluorescence reverse transcription–quantitative polymerase chain reaction.The complete genome of SARS-CoV-2 was sequenced using the MiSeqplatform(Illumina).Multi-sequence alignment analyses were undertaken using Mega 10.1.8 and Dnastar 7.0.1.A phylogenetic tree was constructed with the neighbor-joining method.HN0801 and HN0802 were identified as the Delta variant,and the similarity in the genomic sequence with the reference sequence(NC_045512)was 99.7%and 99.8%,respectively.The phylogenetic tree showed that they were located on different clusters within the same evolutionary branch(B.1.617.2).Forty-five mutation sites on nucleotides caused 38 changes on amino-acid sites;34 missense mutations,six synonymous mutations and four deletions.The spike(S)glycoprotein of SARS-CoV-2 shared common mutational features with the B.1.617.2 lineage(L452R,T478K),as well as the key mutation sites of T19R,G142D,D614G,P681R,D950N and R158G.The gene sequence of HN0801 was 100%identical to that of the representative strain from Nanjing City(Jiangsu Province,China)in July 2021,whereas the genomic similarity between strain HN0802 and the representative strain in Nanjing City was low.According to the epidemiological investigation and genomic sequencing analysis,the two SARS-CoV-2 strains identified in this study were the Delta variant.There was no clear epidemiological correlation between the two confirmed cases.They were independent sporadic cases caused by two different transmission chains.Our data provide a basis for the prevention and control of the Delta variant of SARS-CoV-2 in Hainan Province,China.