全基因组测序在环境样本新型冠状病毒检测中的应用

Application of whole genome sequencing in the detection of SARS-CoV-2 in environmental samples

目的:通过对环境样本进行全基因组测序,为全基因组测序在检测环境标本中SARS-CoV-2的应用提供实践基础,为新冠肺炎疫情的溯源和防控工作提供科学依据。方法:采用新冠病毒全基因组靶向扩增结合Illumina二代测序的技术对5例SARS-CoV-2核酸阳性环境样本进行全基因组测序,应用多种分析软件及在线病毒变异分析平台,判定病毒家系及型别,追溯病毒来源。结果:成功从2份环境样本中获得SARS-CoV-2全基因组序列,均属于B.1.617.2.33进化分支,属于Delta变异株。结论:通过对环境样本进行全基因组测序,不仅能够对病毒进行分型,还能追溯病毒的潜在来源,从分子流行病学角度为贵阳市新冠肺炎疫情的溯源和防控工作提供科学依据。

Objective:Through whole genome sequencing of environmental samples,to provide a practical basis for the application of whole genome sequencing in the detection of SARS-CoV-2 in environmental samples,and to provide a scientific basis for the traceability and prevention and control of the new coronary pneumonia epidemic.Methods:5 SARS-CoV-2 nucleic acid positive environmental samples in Guiyang were carried out by using the technology of whole genome targeted amplification combined with Illumina next-generation sequencing technology,and a variety of analysis software and online virus mutation analysis platform were used to determine the virus family and type,trace the source of the virus.Results:The whole genome sequence of SARS-CoV-2 was successfully obtained from 2 environmental samples,all of which belonged to the B.1.617.2.33 evolutionary branch and belonged to the Delta variant.Conclusion:Whole genome sequencing of environmental samples can not only classify the virus,but also trace the potential source of the virus.From the perspective of molecular epidemiology,it can provide a scientific basis for the traceability and prevention and control of the COVID‑19 Pneumonia Epidemic in Guiyang.