货车司机远距离传播新型冠状病毒肺炎事件的分子溯源

Molecular tracking of long-distance transmission events of COVID-19 by lorry drivers in Fujian province

目的追溯新型冠状病毒肺炎(Coronavirus Disease 2019, COVID-19)病例的感染来源及病毒传播路径, 证实经长途货车司机跨省远距离传播COVID-19事件。方法采用全基因组靶向扩增结合二代测序技术, 对2022年3月福建省泉州市本土疫情暴发期间漳州市报告的5例货车司机COVID-19病例鼻咽拭子标本进行新型冠状病毒(2019 novel coronavirus, 2019-nCoV)全基因组测序, 应用在线分析平台判定病毒型别及突变位点, 利用进化分析软件构建系统发育树, 结合流行病学调查数据, 综合分析病例的感染来源及传播路径。结果成功从5例病例中获得2019-nCoV全基因组序列, 序列长度为29 770~29 839 bp, 基因组平均覆盖度为99.53%;病毒分型结果显示5株病毒均为Omicron变异株, 但分属3种BA.2亚分支;序列分析结果显示3例病毒与2022年3月福建省泉州市本土疫情流行的两种进化分支病毒高度相似, 另2例病毒则与该起疫情流行的病毒存在差异较大(核苷酸突变位点差异7~14个、氨基酸突变位点差异5~7个);进化分析结果表明3例病毒与福建省泉州市本土疫情病毒高度同源, 2例病毒因亲缘关系较远可排除其与泉州市疫情关联;结合病例的个案调查资料, 可以推断至少有2例长途货车司机病例系福建省外感染后返回的散发病例。结论 2019-nCoV全基因组序列分析提示5例COVID-19货车司机病例至少存在3个感染来源, 并推测部分病例系省外感染并跨省长距离传播。

Objective To confirm the cross-provincial long-distance transmission events of Coronavirus Disease 2019(COVID-19)by lorry drivers,the origin of infections of the cases and the transmission routes were tracked.Methods Nasopharyngeal swab specimens from five lorry driver cases of COVID-19,found in Zhangzhou city in March,2022 when the local outbreaks occurred in adjacent Quanzhou city,Fujian province,were collected to perform 2019 novel coronavirus(2019-nCoV)targeted genome amplification and followed by next-generation sequencing.The sequences were submitted to online 2019-nCoV analysis platforms to classify the type of variant and mutation sites.Phylogenetic tree for the viruses were constructed by phylogenetic analysis software.Combined with the epidemiological investigation,the origin of infections of the cases and the transmission routes were deduced.Results Five complete genome sequences,with 29770-29839 bp in length and 99.53%average genomic coverage,of 2019-nCoV were successfully obtained.The viruses were all Omicron variants and further divided into three different subclades of BA.2.Of the five strains of 2019-nCoV,three were highly similar to the viruses of two distinct lineages co-circulated in Quanzhou city during the period of local outbreak of COVID-19,respectively.Phylogenetic analysis also revealed that the viruses from three infected lorry drivers were highly homologous to that from local outbreaks in Quanzhou city.The viruses from the rest two cases had seven to fourteen nucleotide mutations(corresponding to 5-7 amino acid substitutions)when compared with the viruses in local outbreaks in Quanzhou city,which excluded the involvement of the two cases into the transmission chains of local outbreaks.Combined with the field epidemiological investigations,the result revealed that the origin of infection of 2019-nCoV of the two sporadic lorry driver cases was outside of Fujian province.Conclusions With the aid of high-throughput sequencing and bioinformatics technology combined with field epidemiological investigations,we speculated in this study that at least three origins of infection of 2019-nCoV in five lorry driver cases and cross-provincial long-distance transmission via two sporadic cases infected outside Fujian province when they returned.