摘要
目的分析新冠病毒(SARS-CoV-2)奥密克戎(Omicron)变异株流行期间甘肃省天水市本土SARSCoV-2基因组特征和变异情况,为疫情防控提供参考依据。方法收集2022年12月甘肃省天水市新冠病毒感染(COVID-19)重症病例咽拭子样本共136份,采用突变核酸检测试剂盒进行变异株核酸检测,采用二代测序技术进行全基因组测序,Pangolin和Nextclade平台判定病毒谱系及型别,MAFFT软件进行多重序列比对,使用MEGA软件基于邻接法构建系统进化树。结果共获得32条SARS-CoV-2全基因组序列,Pangolin分型31条为Omicron变异株BA.5.2进化分支,1条为Omicron变异株BF.7进化分支;共有68个核苷酸位点和32个氨基酸位点发生突变。S蛋白的受体结合域(RBD)关键位点存在S494P和A522S变异。结论Omicron变异株的编码区突变位点多,编码区的多变异性影响病毒的致病性、传染力和免疫逃逸水平。
Objective To analyze the genomic characteristics and variation of severe acute respiratory disease coronavirus 2(SARS-CoV-2)strains prevalent in a local epidemic of coronavirus disease 2019(COVID-19)in Tianshui city of Gansu province.Methods Pharyngeal swab samples were collected from 136 severe COVID-19 cases in Tianshui city during December 2022.Nucleic acid detection was performed on the isolated SARS-CoV-2 strains with mutant nucleic acid detection kits;whole genome sequencing of the isolated strains was performed using second generation sequencing technology;virus lineage and type were determined with Pangolin and Nextclade platforms and MAFFT software was used for multiple sequences comparison;a phylogenetic tree was constructed using MEGA software with neighbor-joining method.Results Whole genome sequences of 32 isolated SARS-CoV-2 strains were obtained.Pangolin typing analysis showed that of the 32 isolated strains,31 belonged to Omicron variant BA.5.2 evolutionary branch and only one belonged to Omicron variant BF.7 evolutionary branch.Totally 68 nucleotide mutation sites and 32 amino acid mutation sites were identified.The S494P and A522S variants exist in the key sites of the receptor binding domain(RBD)of the S protein.Conclusion There were multiple coding region mutations for the SARS-CoV-2 Omicron virus variants isolated from local COVID-19 patients in Tianshui city and the mutations could affect the pathogenicity,infectivity and immune escape of the prevalent viral stains.
作者
杨雯静
张永斌
赵婧伊
马星宇
YANG Wenjing;ZHANG Yongbin;ZHAO Jingyi;MA Xingyu(Laboratory Department,Tianshui Municipal Center for Disease Control and Prevention,Tianshui 741000,China)
出处
《中国公共卫生》
CAS
CSCD
北大核心
2023年第8期1061-1066,共6页
Chinese Journal of Public Health
