浙江省丽水市一例输入性新型冠状病毒核酸复阳病例的全基因组序列特征

Whole genome sequence of SARS-CoV-2 in one imported re-positive case in Lishui City,Zhejiang Province

目的了解浙江省丽水市一例输入新型冠状病毒(SARS-CoV-2)感染核酸复阳病例的基因组序列特征及变异情况。方法采集该患者的咽拭子和深咳痰液样本,对样本进行病毒核酸提取和实时荧光定量PCR检测,采用高通量测序法对病毒基因组开展测序,对序列进行比对和分析,构建系统进化树,鉴定特异性突变位点。结果获得长度为29815 bp的SARS-CoV-2基因组序列,覆盖病毒编码区全长。同武汉参考株(MN908947)序列相比,存在13个核苷酸突变及一段19 bp长度的缺失,13个核苷酸变异位点没有聚集性。该序列包含了D614G突变,与我国国内本土病例相关性较远,特征符合L基因型欧洲进化分支B.1.1特点,不含有最近南非和英国报道的新型变异毒株的氨基酸关键性突变位点。结论该例SARS-CoV-2感染核酸复阳病例为西班牙输入病例,病毒基因组序列属于L基因型欧洲进化分支B.1.1。

Objective To explore the characteristics of genomic sequence and variation of SARS-CoV-2 in one imported re-positive case in Lishui City,Zhejiang Province.Methods Viral RNA was extracted in throat swab and sputum sample of the patient and was detected by real-time reverse transcription PCR.Viral genome was obtained by high-throughput sequencing.Sequences were compared and analyzed to construct phylogenetic tree and identify specific mutation sites.Results A 29815 bp length of the SARS-CoV-2 genome was obtained covering the entire coding region of the virus.Compared with the Wuhan reference strain(MN908947),there were 13 nucleotide mutations and a lack of 19 bp sequence.The 13 nucleotide mutation sites showed no aggregation.This sequence contained the D614G mutation that was far from the local cases,and was in accord with the lineage B.1.1 which did not contain the key amino acid mutation site reported in South Africa and the UK.Conclusions The imported re-positive case with SARS-CoV-2 infection is from Spain.The viral genome is in the lineage B.1.1.