摘要
目的分析2020年1—2月长沙市疾病预防控制中心微生物实验室收集的2 297份新型冠状病毒(severe acute respiratory syndrome coronavirus 2, SARS-CoV-2)核酸检测基本情况和病毒的分子特征。方法对2020年1月19日—2020年2月29日送至长沙市疾病预防控制中心微生物实验室的新冠肺炎疑似病例咽拭子或呼吸道标本提取病毒RNA,采用实时逆转录聚合酶链反应(real-time reverse transcription polymerase chain reaction, real-time RT-PCR)进行SARS-CoV-2核酸检测;检测阳性标本用SARS-CoV-2全基因组捕获试剂盒进行SARS-CoV-2核酸富集,采用Illumina Miseq测序平台进行病毒全基因组测序,运用SPAdes-3.13.0软件进行序列拼接。从GISAID数据库中下载SARS-CoV-2参考序列进行全基因组遗传进化和抗原变异情况分析。结果共检测临床疑似病例标本2 297份,其中SARS-CoV-2核酸阳性标本215份;阳性病例中,男性110例,女性105例,男女性别比为1.05∶1;40~<60岁年龄组核酸检测阳性率最高(11.35%),6岁以下儿童检出阳性率最低(5.49%)。阳性病例检出高峰为第5周(2020年1月26日—2月1日),后逐渐减少,2020年2月25日后无本土新增病例出现。共获得5条SARS-CoV-2全基因组序列,与武汉参考病毒毒株相比核苷酸突变位点数为4~6个,同源性均在99.90%以上;除C8782T、T28144C 2个突变位点外,其他位点突变仅出现一次,呈现随机性;系统进化分析显示5条序列与同时期国内流行序列高度同源,分属于L/B和S/A 2个基因型。结论通过快速核酸检测和隔离等有效防控措施,长沙市本土SARS-CoV-2的流行在经历约2周的上升期后即开始下降,6周后再无新增确诊病例;全基因组序列分析发现2020年初长沙市流行的SARS-CoV-2与武汉首次报道的病毒高度同源,从输入到本土传播流行期间病毒未出现明显变异。
Objective To analyze the genomics characteristics and nucleic acid detection results of the severe Acute respiratory syndrome coronavirus 2(SARS-CoV-2) in 2 297 clinical samples collected in January and February, 2020 in Laboratory of Microbiology of Changsha Municipal Center for Disease Control and Prevention. Methods Viral RNA of throat swabs or respiratory tract specimens of coronavirus disease 2019(COVID-19) suspected cases from January 19, 2020 to February 29, 2020 was extracted and SARS-CoV-2 nucleic acid was detected by real-time reverse transcription polymerase chain reaction.The full length genome of SARS-CoV-2 in positive samples was enriched by using viral genome capture kit and sequenced on Illumina MiSeq platform.The raw reads were mapped and aligned with SPAdes software v 3.13.0.Reference SARS-CoV-2 sequences were obtained from GISAID(https://www.gisaid.org) andviral genetic evolution and antigen variation were analyzed. Results A total of 215 SARS-Co V2-nucleic acid positive samples were identified from 2 297 clinical samples.Among the SARS-Co V2-positive samples, 110 were males and 105 were from females.The male to female ratio was 1.05∶1.The highest positive rate was among 40—<60 years old people(11.35%) and the lowest positive rate was in children under 6 years old(5.49%).The peak of newly confirmed cases was in the 5 th week(January 26 to February 1, 2020) and then decreased.There was no newly positive case after February 25, 2020.Five SARS-Co V2-whole genome sequences were obtained and there were 4 to 6 nucleotide mutations compared to the Wuhan reference strain, and the homology was more than 99.90%.Most mutations occurred only once except C8782 T and T28144 C, indicating random mutations.Phylogenetic analysis revealed that the 5 sequences belonged to the L/B or S/A lineages and were highly homologous with strains prevalent in other provinces of China at the same time. Conclusions With the quick nucleic acid tests and quarantine measures, the SARS-Co V2-positive cases in Changsha began to decline after a 2-week increasing period, and there was no new confirmed cases 6 weeks later.The genomes of SARS-Co V-2 prevalent in Changsha are highly homology with the Wuhan strains in the early 2020 and no obvious mutation is found in the local pandemic period.
作者
陈静芳
徐明忠
张如胜
欧新华
黄政
姚栋
CHEN Jing-fang;XU Ming-zhong;ZHANG Ru-sheng;OU Xin-hua;HUANG Zheng;YAO Dong(Lab of Microbiology,Center for Disease Control and Prevention of Changsha City,Changsha,Hunan 410008,China)
出处
《中国病毒病杂志》
CAS
2021年第6期455-459,共5页
Chinese Journal of Viral Diseases
基金
湖南省创新型省份建设专项(2020SK3046)
湖南省卫生健康委员会科研计划项目(202012060458)
长沙市自然科学基金项目(kq2014018)
长沙市卫生计生委科研计划课题项目。
关键词
新型冠状病毒
核酸检测
全基因组测序
分子特征
SARS-CoV-2
Nucleic acid test
Whole genome sequencing
Molecular characteristics
