河南省2021年境外输入SARS-CoV-2全基因组测序分析

Analysis of whole genome of SARS-CoV-2 imported from abroad in Henan Province in 2021

目的:分析河南省2021年境外输入新型冠状病毒SARS-CoV-2的全基因组特征和变异情况。方法:收集河南省2021年85份境外输入SARS-CoV-2阳性标本,采用新冠病毒全基因组靶向扩增结合二代测序技术进行全基因组测序,应用CLC Genomics Workbench 20软件进行变异分析,应用进化分析在线平台,采用邻近法构建系统发育进化树。结果:共获得85株病毒,其中非关切变异株(VOC)、Alpha、Beta、Delta和Omicron变异株占比分别为4.71%、10.59%、2.35%、76.47%和5.88%,未发现Gamma变异株输入。非VOC、Alpha、Beta、Delta和Omicron病毒株累计核苷酸突变数和氨基酸突变数分别为59、77、36、288、72个和40、46、20、171、50个。85株均存在C241T、C3037T、C14408T、A23403G核苷酸突变和P4715L、D614G氨基酸突变。系统发育树显示,85株具有基因型多样性,各VOC型病毒株序列形成不同的进化分支,Delta病毒株可形成多种类型的亚分支,且入境来源具有明显的地域性。结论:2021年河南省境外输入的SARS-CoV-2以Delta病毒株为主,基因组突变呈现随机性和多样性。

Aim:To investigate the whole genome characteristics and variations of SARS-CoV-2 imported from abroad in Henan Province in 2021.Methods:The SARS-CoV-2 positive samples from 85 imported cases in Henan Province in 2021 were performed the whole genome sequencing for SARS-CoV-2 using the targeted genome amplification combined with second-generation sequencing technology,and the CLC Genomics Workbench 20 software was used to analyze the variation sites in the whole genome of the virus.The phylogenetic tree was constructed by Neighbor-Joining method using the online platform of evolutionary analysis.Results:A total of 85 strains were obtained,among which,the non-variants of concern(non-VOC),Alpha,Beta,Delta and Omicron variants accounted for 4.71%,10.59%,2.35%,76.47%and 5.88%,respectively.No Gamma virus strain was found.The total number of non-VOC,Alpha,Beta,Delta and Omicron nucleotide mutations and amino acid mutations was 59,77,36,288,72 and 40,46,20,171 and 50,respectively.All 85 strains had C241T,C3037T,C14408T,A23403G nucleotide mutations,and P4715L,D614G amino acid mutations.Phylogenetic tree analysis showed that 85 strains had genotypic diversity,and each VOC strain formed different evolutionary branches,and Delta strain could form multiple types of sub-branches,and the entry source had obvious regional characteristics.Conclusion:In 2021,the imported SARS-CoV-2 strain in Henan Province were mainly Delta,and the genome mutations showed randomness and diversity.