3例境外新冠病毒感染者的病毒全基因组测序分析

Whole genome sequencing analysis of 3 abroad cases of SARS-CoV-2 infection

目的了解境外新冠病毒全基因组特征和变异情况,及时发现境外流行新冠病毒变异类型,为云南省边境州市制定针对性的防控策略提供科学依据。方法2021年11月,采集与云南省瑞丽市接壤的缅甸3例新冠病毒感染者的鼻咽拭子样本,提取核酸进行病毒全基因组测序,以新冠病毒武汉株Wuhan-Hu-1(NC_045512)为参考序列进行比对分析。结果成功从3份样本中获得长度为29881 bp、29852 bp、29875 bp的新冠病毒全基因组序列,基因组覆盖度为99.90%、99.87%、99.99%,分别检出39个、40个、45个碱基位点突变,涉及28个、26个、28个氨基酸变异,非同义突变占66.1%(82/124),以ORF1ab基因占比最高,达37.8%(31/82)。序列比对显示3个境外感染者的病毒序列与云南同一时间监测的病毒基因组序列高度同源,系统发育树显示3个境外感染者和瑞丽本土疫情病例聚成一簇。结论3个境外新冠病毒感染者的病毒均属Delta变异株(B.1.617.2进化分支),未监测到其他类型变异毒株。瑞丽市本土疫情的持续传播可能与边境人员和缅甸病例直接或者间接接触有关。

Objective To understand the whole genome characteristics and variation of SARS-CoV-2 from foreign countries,and to find out the epidemic of SARS-CoV-2 in foreign areas in time,so as to provide scientific basis for formulating targeted prevention and control strategies in border prefectures and cities of Yunnan Province.Methods The nasopharyngeal swab samples of 3 cases with SARS-CoV-2 infection in Myanmar bordering Ruili,Yunnan Province were collected,and nucleic acid was extracted for whole genome sequencing.SARS-CoV-2 strain Wuhan-Hu-1(NC_045512)was used as the reference sequence for comparative analysis.Results The whole genome sequences of SARS-CoV-2 with 29881 bp,29852 bp and 29875 bp were successfully obtained from the 3 samples.The genome coverage was 99.90%,99.87%and 99.99%,respectively.39,40 and 45 base site mutations were detected,involved 28,26 and 28 amino acid mutations.Non-synonymous mutations accounted for 66.1%(82/124)and ORF1ab gene accounted for the highest proportion reached 37.8%(31/82).Sequence alignment showed that the viral sequences of the 3 abroad cases were highly homologous to the viral genome sequences monitored in Yunnan at the same time.Phylogenetic tree showed that the 3 abroad infected cases and the local epidemic cases in Ruili clustered together.Conclusion The viruses of the 3 abroad infections belonged to the Delta variant(B.1.617.2 evolutionary branch),no other types of variants were detected.The continuous spread of the local epidemic in Ruili might be related to direct or indirect contact between border personnel and Myanmer cases.