四川省首例猴痘病例病毒基因组特征分析  

Genetic characteristics of mpox virus from the first mpox case in Sichuan

作　　者：曹冉冉[1] 刘晨霞 罗灿 徐朝花 刘李[1] 潘明[1] Cao Ranran;Liu Chenxia;Luo Can;Xu Chaohua;Liu Li;Pan Ming(Microbiology Institution,Sichuan Center for Disease Control and Prevention,Chengdu 610041,Sichuan,China)

机构地区：[1]四川省疾病预防控制中心微生物检验所,四川成都610041

出　　处：《疾病监测》2024年第8期989-994,共6页Disease Surveillance

基　　金：四川省科技厅重点研发项目(No.2022YFS0637,No.2023YFS0501,No.2023YFS0502)。

摘　　要：目的 分析四川省首例猴痘病例感染病毒全基因组特征,为猴痘防控工作提供基础资料。方法 采集病例咽拭子和疱疹液拭子提取核酸,用实时荧光聚合酶链式反应(PCR)进行初筛,确认阳性后用纳米孔测序进行全基因组测序。测序数据用Minimap2 v2.18-r1015、Medaka v1.8.0、Snpeff v4.3.1软件进行组装、核苷酸突变位点识别和功能注释,通过在线分析平台Nextclade(https://clades.nextstrain.org/)进行型别鉴定,以IQ-TREE v2.1.2软件构建全基因组进化树。结果 3种实时荧光PCR试剂盒检测咽拭子和疱疹液拭子均显示猴痘病毒核酸阳性,且疱疹液拭子每个反应管内荧光信号达到设阈值时所经历的循环数(Ct值)均低于咽拭子。全基因组测序分析显示,该病例感染的猴痘病毒(SC001)属于IIb分支B.1.3基因型,与美国、日本、中国浙江省等地流行的毒株同源(核苷酸相似性99.98%~99.99%),其中与浙江省流行的毒株最为相近(核苷酸相似性99.99%)。与参考基因组(NC_063383.1)相比,SC001株含有70个单核苷酸突变位点。结论 四川省首例猴痘病例感染的病毒与我国其他地区流行株的基因型一致,后续应持续关注病毒遗传进化情况,警惕新变异株出现。Objective To analyze the genetic characteristics of the mpox virus(MPXV)isolated from the first mpox case in Sichuan.Methods Oropharyngeal swab and skin lesion swab were collected from the case to extract MPXV nucleic acid for real-time polymerase chain reaction(PCR)test.After confirmed the positive PCR results,nanopore sequencing was used to sequence the whole genome of MPXV.Minimap2(v2.18-r1015),Medaka(v1.8.0)and Snpeff(v4.3.1)were used to analyze sequence data.Nextclade(https://clades.nextstrain.org/)was used for the genotype identification.IQ-TREE(v2.1.2)was used to construct phylogenetic tree.Results The oropharyngeal swab and skin lesion swab collected from the case were positive for MPXV tested by three real-time PCR kits.The cycle threshold(Ct)value of the skin lesion swab was lower than that of the oropharyngeal swab by three real-time PCR kits.Whole genome sequencing analysis revealed that the MPXV strain from this case belonged to lineage B.1.3 in clade IIb.Phylogenetic analysis showed that the strain was homologous to those identified in the United States,Japan,and Zhejiang province of China with nucleotide similarity between 99.98%and 99.99%.The strain shared the highest nucleotide similarity(99.99%)with the strain from Zhejiang.Compared to the reference genome(NC_063383.1).The strain carried 70 nucleotide substitutions.Conclusion The genetic characteristics of MPXV detected in Sichuan were similar to those detected in other areas of China.It is vital to strengthen surveillance for the genetic characteristics of MPXV for the timely detection of new variants.

关 键 词：猴痘 猴痘病毒 全基因组测序 纳米孔测序 

分 类 号：R211[医药卫生—中医学] R373.9