摘要
目的对呼和浩特市6例确诊为SARS-CoV-2感染患者进行全基因组测序,了解病毒特征,追溯病毒来源。方法采用Nanopore三代高通量测序技术对6份咽拭子样本进行病毒基因组测序,基于ARTIC病毒基因组组装流程,使用生物信息学软件将病毒序列与参考序列进行比对,分析进化情况。结果获得4份样本的全基因组序列,均属于SARS-CoV-2变异株Delta(B.1.617.2-like),Pangolin分型为AY.122。测序时长1.5 h/样本,测序长度27009~29560 bp,覆盖度90.32%~98.85%。共鉴定出50个碱基位点突变、46处氨基酸变异,错义突变占比74%(37/50),错义突变中以ORF1ab基因占比最高45.95%(17/37)。结论Nanopore单分子测序技术在病毒全基因组测序中具有读长长、测序时间短的特点。与武汉参考株比对发现,该病毒的核苷酸位点变异存在多态性,要密切关注病毒变异情况,切实做好防控措施。
Objective To understand the characters of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)and trace the source of the virus by whole genome sequencing for six confirm SARS-CoV-2 infected patients in Hohhot.Methods Six throat swab samples were sequenced by Nanopore third-generation high-throughput sequencing technology.Based on the ARTIC virus genome assembly process,bioinformatics software was used to compare the virus sequences with the reference sequence and in phylogenetic analysis.Results Four complete genomes were obtained,and all belonged to the Delta variant(B.1.617.2-like)of SARS-CoV-2,and the Pangolin type was AY.122.The sequencing time was 1.5 h per sample,the sequencing length was 27009-29560 bp.The coverage was 90.32%-98.85%.A total of 50 point mutation sites and 46 amino acid mutations were identified.The non-synonymous mutations accounting for 74%(37/50),and ORF1ab gene accounted for the highest proportion of 45.95%(17/37)for the mutation.Conclusions Nanopore single-molecule sequencing technology is characterized by long read length and short sequencing time in virus whole genome sequencing.Compared with the Wuhan reference strain,polymorphism existed in the point mutations of the virus.Close attention should be focused on the virus mutation and take effective prevention and control measures.
作者
王波
李晓聪
肖伟利
李慧君
丁海涛
Wang Bo;Li Xiaocong;Xiao Weili;Li Huijun;Ding Haitao(Department of Laboratory Medicine,Inner Mongolia People's Hospital,Hohhot 010017,China)
出处
《国际病毒学杂志》
2023年第2期110-114,共5页
International Journal of Virology
基金
内蒙古自治区卫生健康委医疗卫生科技计划项目(202201054)。
