2022年海南省新型冠状病毒奥密克戎(BA.1.1)变异株基因特征分析

Analysis of Genetic Characteristics of Omicron Variant of SARS-CoV-2 in 2022 in Hainan Province,China

为进一步积累和完善海南省新型冠状病毒(Severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)奥密克戎(Omicron)变异株病原学特点的认识,本研究对2022年海南省14例感染奥密克戎(BA.1.1)变异株病例进行新冠病毒基因特征分析。应用Illumina公司MiSeqDX深度测序平台进行全基因组序列测定,Nextclade在线分析平台和DNASTAR 7.0.1生物信息学软件进行多序列比对和基因组特征分析,采用MEGA 10.1.8邻位归并法(Neighbour-joining)绘制系统进化树,结合流行病学调查进行回顾性溯源分析。海南省14例病例感染的奥密克戎(BA.1.1)变异株基因组高度相似,同武汉参考序列(GenBank No.NC_045512)相比,存在63或64个核苷酸突变位点,39个核苷酸位点缺失,22204位点有9个核苷酸插入,引起43个氨基酸突变和16个氨基酸位点缺失。刺突(Spike,S)蛋白存在32个氨基酸突变位点,S1蛋白RBD区R346K是VOC/Omicron(BA.1.1)变异株特征性突变位点。14例病例分布在三亚市及外溢到周边陵水、儋州等市县,均为外省来琼感染者引发后续本地传播。海南省因输入病例引起本土新冠疫情的风险较大,应继续加强新冠病毒重要流行变异株的研究,持续开展新冠病毒基因型变异监测。

In order to further accumulate and improve the understanding of the pathogenic characteristics of SARS-CoV-2 Omicron variant in Hainan Province,China,this study analyzed the epidemiological and genomic characteristics of 14 cases infected with Omicron variant(BA.1.1),which was found in 2022 in Hainan Province,China.The Illumina MiSeq platform was used to sequence the whole genome.The Nexttrade online analysis platform and DNASTAR 7.0.1 software were applied to perform multiple sequence alignment.The MEGA 10.1.8 method was used to create the Neighbor-joining phylogenetic tree.The genomes of the 14 strains in Hainan Province(China) were remarkably similar.In comparison to the Wuhan reference sequence(GenBank No.NC 045512),the Hainan SARS-CoV-2 genome included 63 or 64 nucleotide mutation sites,39 nucleotide deletion sites,and 9 nucleotide insertions at position 22204,leading to 43 amino acid mutations and 16 amino acid deletion sites.There were 32 amino acid mutation sites in S(spike) protein,and R346K in RBD region of S1 protein is the characteristic mutation site of VOC/Omicron(BA.1.1) mutant.The epidemiological survey found that 14 local cases spread from Sanya City,China to the neighboring cities of Lingshui,China and Danzhou,China,all of which were imported from other provinces and led to local transmission.In Hainan Province,China,there is considerable chance of a local epidemic situation as a result of imported cases.The genome sequencing of SARS-CoV-2 must be strengthened in order to get necessary fundamental information for the surveillance of SARS-CoV-2 variants in Hainan Province,China.