新型冠状病毒Alpha变异株实验室检测研究  

Study on the laboratory diagnosis of the Alpha variant of SARS-CoV-2

作　　者：龚甜[1] 余福平 李健雄[1] 施勇[1] 刘师文[1] 肖芳[1] 熊火梅 肖大瑾 刘晓庆[1] 张艳妮[1] 徐刚[1] 周珺[1] 冉鑫 王倩 熊英[1] GONG Tian;YU Fu-ping;LI Jian-xiong;SHI Yong;LIU Shi-wen;XIAO Fang;XIONG Huo-mei;XIAO Da-jin;LIU Xiao-qing;ZHANG Yan-ni;XU Gang;ZHOU Jun;RAN Xin;WANG Qian;XIONG Ying(Jiangxi Center for Disease Control and Prevention,Nanchang,Jiangxi 330029,China)

机构地区：[1]江西省疾病预防控制中心,江西南昌330029 [2]九江市疾病预防控制中心,江西九江332000

出　　处：《现代预防医学》2022年第14期2652-2655,2688,共5页Modern Preventive Medicine

摘　　要：目的对一例新冠肺炎境外输入病例进行实验室检测,并对新型冠状病毒(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)变异株进行鉴定,了解不同样本类型中新冠病毒的检出情况。方法采集咽拭子、痰液、粪便、尿液和血液多种类型样本共13份,分别提取核酸,用荧光RT-PCR法检测SARS-CoV-2。使用纳米孔MinION Mk1C测序仪,对阳性咽拭子样本进行实时SARS-CoV-2靶向扩增全基因组测序,运用artic-ncov2019、DNAstar和Mega等软件对测定序列进行处理和分析。结果咽拭子、痰液、粪便、血浆和尿沉渣样本中均检出SARS-CoV-2核酸,咽拭子和血浆样本在发病的前四天均能检出,尿沉渣样本在发病当天能检出。基于纳米孔测序技术,7 h即获得SARS-CoV-2全基因组数据,经分析显示为新冠病毒Alpha变异株。结论本例境外输入新冠肺炎确诊病例的病原为SARS-CoV-2 Alpha变异株,咽拭子、血浆样本和尿沉渣样本在发病早期均能检出SARS-CoV-2核酸。Objective To perform laboratory tests on an imported COVID-19 case outside China and to identify a novel coronavirus(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)variant for the detection of the virus in different sample types.Methods A total of 13 samples of various types of pharyngeal swabs,sputum,stool,urine,and blood were collected.Nucleic acids were extracted and SARS-CoV-2 was detected by fluorescence RT-PCR.Real-time SARS-CoV-2targeted amplification whole genome sequencing was performed on positive pharyngeal swab samples using a nanopore MinION Mk1C sequencer.Artic-ncov2019,DNAstar,and Mega software were used to process and analyze the determined sequences.Results SARS-CoV-2 nucleic acid was detected in throat swab,sputum,stool,plasma and urine sediment samples.SARS-CoV-2 nucleic acid was detected in throat swab and plasma samples in the first four days of onset,and in urine sediment samples on the day of onset.Based on nanopore sequencing technology,SARS-CoV-2 whole genome data were obtained in 7 hours,which were analyzed and shown to be the Alpha variant.Conclusion The pathogen of this confirmed case of overseas imported novel coronavirus pneumonia is SARS-CoV-2 Alpha variant,and SARS-CoV-2 nucleic acid is detected in pharyngeal swabs,plasma samples,and urine sediment samples in the early onset of the disease.

关 键 词：新型冠状病毒 Alpha变异株 血浆 尿沉渣 纳米孔测序技术 

分 类 号：R563.1[医药卫生—呼吸系统]