Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing  

作　　者：Changcheng Wu Ruhan A Sheng Ye Fei Ye Weibang Huo Roujian Lu Yue Tang Jianwei Yang Xuehong Meng Yun Tang Shuang Chen Li Zhao Baoying Huang Zhongxian Zhang Yuda Chen Dongfang Li Wenling Wang Ke-jia Shan Jian Lu Wenjie Tan 

机构地区：[1]NHC Key Laboratory of Biosafety,National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention,Beijing,100052,China [2]Chongqing Municipal Key Laboratory for High Pathogenic Microbes,Chongqing Center for Disease Control and Prevention,Chongqing,400042,China [3]MGI,BGI-Shenzhen,Shenzhen,518083,China [4]Thermo Fisher Scientific,Beijing,100013,China [5]School of Public Health,Baotou Medical College,Baotou,014030,China [6]BGI PathoGenesis Pharmaceutical Technology,Shenzhen,518000,China [7]State Key Laboratory of Protein and Plant Gene Research,Center for Bioinformatics,School of Life Sciences,Peking University,Beijing,100871,China [8]College of Life Sciences,University of Chinese Academy of Sciences,Beijing,100049,China

出　　处：《Virologica Sinica》2024年第1期134-143,共10页中国病毒学（英文版）

基　　金：supported by the National Key Research and Development Program of China(2022YFC2303401,2022YFC2304100,2016YFD0500301,2021YFC0863300);the Beijing Science and Technology Plan(Z211100002521017);the National Natural Science Foundation of China(82241080)。

摘　　要：The monkeypox virus(MPXV)has triggered a current outbreak globally.Genome sequencing of MPXV and rapid tracing of genetic variants will benefit disease diagnosis and control.It is a significant challenge but necessary to optimize the strategy and application of rapid full-length genome identification and to track variations of MPXV in clinical specimens with low viral loads,as it is one of the DNA viruses with the largest genome and the most AT-biased,and has a significant number of tandem repeats.Here we evaluated the performance of metagenomic and amplicon sequencing techniques,and three sequencing platforms in MPXV genome sequencing based on multiple clinical specimens of five mpox cases in Chinese mainland.We rapidly identified the full-length genome of MPXV with the assembly of accurate tandem repeats in multiple clinical specimens.Amplicon sequencing enables cost-effective and rapid sequencing of clinical specimens to obtain high-quality MPXV genomes.Third-generation sequencing facilitates the assembly of the terminal tandem repeat regions in the monkeypox virus genome and corrects a common misassembly in published sequences.Besides,several intra-host single nucleotide variations were identified in the first imported mpox case.This study offers an evaluation of various strategies aimed at identifying the complete genome of MPXV in clinical specimens.The findings of this study will significantly enhance the surveillance of MPXV.

关 键 词：Monkeypox virus(MPXV) METAGENOMIC Next generation sequencing AMPLICON Third-generation sequencing 

分 类 号：R373[医药卫生—病原生物学]