长沙市4例输入新型冠状病毒Omicron变异株全基因组序列特征分析  

Characteristics of full-genome sequence of four imported Omicron variants of SARS-CoV-2 in Changsha City

作　　者：黄政[1] 徐明忠[1] 欧新华[1] 向星宇[2] 湛志飞[2] 姚栋[1] HUANG Zheng;XU Ming-zhong;OU Xin-hua;XIANG Xing-yu;ZHAN Zhi-fei;YAO Dong(Changsha Municipal Center for Disease Control and Prevention,Changsha,Hunan 410004,China;Hunan Provincial Center for Disease Control and Prevention,Changsha,Hunan 410000,China)

机构地区：[1]湖南省长沙市疾病预防控制中心,湖南长沙410004 [2]湖南省疾病预防控制中心,湖南长沙410000

出　　处：《实用预防医学》2022年第12期1431-1434,共4页Practical Preventive Medicine

基　　金：湖南省卫生健康委科研课题项目(202012060458),“基于污水、环境及临床病例SARS-CoV-2监测对长沙市COVID-19疫情预警可行性研究”。

摘　　要：目的 分析长沙市境外输入新型冠状病毒(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)的全基因组序列特征以及遗传变异情况。方法 采用高通量测序方法对2021年12月的SARS-CoV-2进行全基因组序测序,序列进行比对以及进化分析。结果 本研究获得4株SARS-CoV-2全基因组序列,长度为29 685 bp。毒株核苷酸序列与Wuhan-Hu-1参考株(EPI_ISL_402125)相比,同源性为99.6%。与Omicron变异株(EPI_ISL_8890653)相比,同源性为99.9%。进化树分析表明毒株序列位于BA.1.1分支,与SARS-CoV-2 Omicron变异株位于同一分支。氨基酸序列位点分析发现毒株具有典型的Omicron序列突变位点。ORF1ab区域发现G5494S,K4346R,T5035I和E6945D突变。S蛋白抗体结合区域发生R346K突变。结论 长沙市输入的Omicron变异株携带已报道可明确导致病毒传播和致病力发生变化的突变位点,应继续加强疫情应对措施。Objective To analyze the characteristics and genetic variation based on full-genome of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) from imported cases in Changsha City.Methods The high-throughput sequencing technology was used to perform whole genome sequencing of SARS-CoV-2 isolated in December 2021.Nucleotide sequences were compared,and phylogenetic analysis was conducted.Results Genome sequences of four SARS-CoV-2 strains were obtained in this research.The full length of genome sequences was 29,685 bp.Based on nucleotide sequences,homology comparison showed that four SARS-CoV-2 strains shared 99.6% and 99.9% similarity with Wuhan-Hu-1 reference strain(EPI_ISL_402125) and Omicron strain(EPI_ISL_8890653),respectively.Phylogenetic analysis revealed that the strains belonged to BA.1.1 branch which SARS-CoV-2 Omicron variants presented.The amino acid sequences revealed that four SARS-CoV-2 strains contained the mutation sites that had been reported in Omicron variants.We also found some novel substitution sites in ORF1 ab amino acid sequences,including G5494 S,K4346 R,T5035 I and E6945 D,and R346 K novel substitution in receptor-binding domain of S sequences.Conclusion The imported Omicron variants of SARS-CoV-2 in Changsha City contained all representative mutation sites that had been reported to increase the viral transmission and pathogenicity.We should continue to strengthen prophylactic measures against SARS-CoV-2.

关 键 词：新型冠状病毒 奥密克戎 全基因组序列 进化分析 

分 类 号：R373.9[医药卫生—病原生物学]