新型冠状病毒Alpha变异株实验室检测研究

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。

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

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-2 targeted 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.