2021年宁夏境外输入和本土SARS⁃CoV⁃2流行病学与基因组特征研究

Epidemiological and Genetic Characteristics of Imported and Local SARS⁃CoV⁃2 in Ningxia,China,in 2021

研究宁夏境外输入性和本土SARS⁃CoV⁃2感染者流行病学特征及其感染病毒的基因组变异特征,为防控策略的制定和病毒溯源提供参考依据。境外输入感染者信息来源于中国疾病预防控制信息系统传染病报告信息管理系统,收集2021年宁夏入境新冠病毒核酸阳性人员信息和本地区新冠疫情的流行病学报告,采用Illumina Miseq平台上进行高通量测序,用Mafft对基因组序列多重比对,用RAxML构建最大似然法进化树(GTR+G模型,bootstrap=1000)。2021年宁夏共报告50例新冠病毒核酸阳性感染者,其中境外输入5例,本土疫情感染者45例。男性20例,女性30例;年龄小于18岁4例,18~30岁6例,30~49岁10例,大于等于50岁26例。11例病例未接种新冠肺炎疫苗,其他均完成2针剂的新冠肺炎疫苗的免疫程序。无症状感染者为4例,确诊病例为46例。获得47例病例全基因组序列,测序结果显示均为Delta变异株,境外输入病例核苷酸变异位点与10月疫情病例具有明显差异,系统进化树在不同的分支,10月疫情聚集于一簇。Delta变异株具有病毒载量高,传播速度快的特点,境外输入SARS⁃CoV⁃2变异株存在引起本地暴发与流行的风险。

To study the epidemiological and genetic characteristics of imported and local severe acute respiratory syndrome⁃coronavirus⁃2(SARS⁃CoV⁃2)infections in Ningxia,China.We wished to provide a reference for creating prevention⁃and⁃control strategies and tracing the source of new outbreaks.Information on imported and local SARS⁃CoV⁃2 infections were obtained from the management system of the Chinese Center for Disease Control and Prevention.Information on imported epidemics in Ningxia in 2021 and epidemiological reports of local epidemics was collected.High⁃throughput sequencing was done on the MiSeq platform(Illumina).Mafft was used for multiple alignment of genome sequences.RAxML was employed to construct a maximum⁃likelihood phylogenetic tree(GTR+G model,bootstrap=1000).Fifty cases of SARS⁃CoV⁃2 infections were documented in 2021:five imported cases and 45 local cases.There were 20 males and 30 females;four cases were younger than 18 years of age,six cases were aged 18–30 years,10 cases were aged 30–49 years,and 26 cases were aged≥50 years.Eleven cases had not completed vaccination against SARS⁃CoV⁃2,but the remaining cases had.Four asymptomatic infections and 46 confirmed cases were documented.In 47 cases,sequences of the whole genome were obtained,and showed that they were all the Delta mutant strain.The mutations of nucleotides of imported cases were significantly different from those of local epidemic cases in October,and were distributed in different branches of the phylogenetic tree.All the sequences of SARS⁃CoV⁃2 in the local epidemic were gathered in a large cluster in October.The Delta variant of SARS⁃CoV⁃2 had a high viral load and was transmitted rapidly.Imported SARS⁃CoV⁃2 variants may cause local outbreaks and epidemics.