输入性新冠病毒奥密克戎XBB.1型全基因组测序及特征

Whole genome sequencing and characterization of imported SARS-CoV-2 Omicron XBB.1 variant

目的 针对江苏口岸1例境外输入性新冠病毒(SARS-CoV-2)感染者咽拭子样本,通过二代测序技术进行全基因组测序及序列分析,掌握输入性SARS-CoV-2基因型及分子特征,为口岸新冠病毒防控提供理论支持。方法 通过荧光定量PCR和二代测序技术对入境感染者咽拭子样本进行新冠病毒核酸检测,对Ct≤32的阳性样本开展全基因组测序。结果 获得1株输入性SARS-CoV-2全基因组序列(GenBank:OQ048285),基因组全长29 772 bp,基因型为奥密克戎XBB.1型。与参考毒株(GenBank:NC_045512.2)相比,该毒株有56个碱基位点缺失,有88个位点发生了替换;氨基酸缺失位点有13个,突变位点有63个。结论 奥密克戎XBB.1型是江苏口岸首次检出的输入性新冠病毒基因型,为当地口岸新冠病毒的防控及分子溯源提供重要技术支持。

Objective To carry out whole genome sequencing and characterization of throat swab sample collected from 1 case of SARS-CoV-2 infection at Jiangsu port,so as to provide scientific basis for the prevention and control of SARS-CoV-2 at ports.Methods SARS-CoV-2 nucleic acid detection was performed on throat swab sample of inbound infection by fluorescent quantitative PCR and whole genome sequencing was performed on positive sample with Ct≤32 by second-generation sequencing technology.Results A complete genome sequence of SARS-CoV-2 was obtained(GenBank:OQ048285),with full length of 29772 bp.The strain was Omicron XBB.1 variant.Comparing with the original strain(GenBank:NC_045512.2),there were 56 deleted bases and 88 mutated bases,corresponding with 13 amino acid deletions and 63 amino acid mutations.Conclusion Omicron XBB.1 was the first imported SARS-CoV-2 genotype detected at Jiangsu port,providing an important scientific basis for the tracing,prevention and control of SARS-CoV-2 at local ports.