云南省陇川县本土新冠疫情溯源和病毒基因组变异解析

Origin of the COVID-19 Outbreak in Longchuan County,Yunnan Province,China,and Analyses of Variation in the SARS-CoV-2 Genome

2021年7月14日,云南省陇川县报告了新型冠状病毒肺炎(COVID-19)本土疫情。为了阐明本次德宏州陇川县本土疫情的感染来源和SARS-CoV-2变异情况,我们收集疫情期间采集的9例陇川疫情本土病例和2例陇川境外病例标本进行新冠病毒全基因组测序。通过一系列比较基因组学分析,发现9例陇川疫情本土病例和2例陇川境外病例病毒株基因组序列高度同源,均属Delta变异株(B.1.617.2进化分支),在系统发育树上单独成簇,为同一传播链。9例陇川疫情本土病例和2例境外病例病毒株基因组序列共享38个SNP突变位点和13个缺失。9例本土病例中的4例病毒株均额外增加了1个共享的SNP突变位点,其中2例本土病例病毒株新产生9个核苷酸缺失。这些病毒株S蛋白均发现L452R、T478K、P681R等可能影响病毒传播和免疫逃逸能力的关键性变异位点。该研究表明本次陇川疫情的暴发与发病前14天内德宏州陆路口岸输入病例以及瑞丽2021年7月14日疫情本土病例并无关联性,提示病毒传染源可能来自境外人员。因此,应持续加强边境从业人员和抵边村寨边民的病毒核酸检测以及本土/输入病例基因组变异规律的深入挖掘和监测。

On 14 July 2021,a local outbreak of coronavirus disease 2019(COVID-19)was reported in Longchuan County(Yunnan Province,China).We wished to clarify the source of infection and genomic variations of severe acute respiratory-coronavirus-2(SARS-CoV-2)from the local epidemic in Longchuan County in Dehong Prefecture(Yunnan Province,China).Nine samples from local cases in Longchuan and two samples from cases in Myanmar during the epidemic were collected for whole-genome sequencing.Comparative genomics analysis revealed the genome sequences of the nine local cases in Longchuan County and two cases from abroad to be highly homologous.Both belonged to the Delta variant strain in the B.1.617.2 lineage,which evolved into monophyletic branches in our phylogenetic tree and were the same transmission chain.The genome sequences of SARS-CoV-2 from the nine local cases and two cases from Myanmar shared 38 single-nucleotide polymorphism(SNP)mutation sites and 13 deletions.Four of the nine local cases had an additional shared SNP mutation site,and two of the four local cases had nine new deletions.The vital mutation sites(e.g.,L452R,T478K and P681R)were located in the S protein for these virus strains,which may affect the transmission and“immune escape”ability of the Delta variant of SARS-CoV-2.We showed that the COVID-19 outbreak in Longchuan County did not harbor a significant correlation with the cases imported via land ports in Dehong Prefecture or the local cases of the Ruili On 14 July 2021,outbreak within 14 days,which suggested that the source of infection for the Longchuan epidemic might be from overseas personnel.Therefore,testing of the nucleic acids of SARS-CoV-2 must be strengthened for the workers and residents of border villages,as well indepth excavation and monitoring of variations within the SARS-CoV-2 genome for local or imported cases.