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

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

doi:10.1016/j.virs.2023.12.002

February 2024

Citation: 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. Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing .VIROLOGICA SINICA, 2024, 39(1) : 134-143. http://dx.doi.org/10.1016/j.virs.2023.12.002

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

Changcheng Wu ^a ,
Ruhan A ^a ,
Sheng Ye ^b ,
Fei Ye ^a ,
Weibang Huo ^a ,
Roujian Lu ^a ,
Yue Tang ^c,h ,
Jianwei Yang ^c ,
Xuehong Meng ^d ,
Yun Tang ^b ,
Shuang Chen ^b ,
Li Zhao ^a ,
Baoying Huang ^a ,
Zhongxian Zhang ^a,e ,
Yuda Chen ^a,e ,
Dongfang Li ^f ,
Wenling Wang ^a ,
Ke-jia Shan ^g ,
Jian Lu ^{g
,,} ,
Wenjie Tan ^{a,e
,,}

a. NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China;
b. Chongqing Municipal Key Laboratory for High Pathogenic Microbes, Chongqing Center for Disease Control and Prevention, Chongqing, 400042, China;
c. MGI, BGI-Shenzhen, Shenzhen, 518083, China;
d. Thermo Fisher Scientific, Beijing, 100013, China;
e. School of Public Health, Baotou Medical College, Baotou, 014030, China;
f. BGI PathoGenesis Pharmaceutical Technology, Shenzhen, 518000, China;
g. State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China;
h. College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China

Corresponding author: Jian Lu, luj@pku.edu.cn
Wenjie Tan, tanwj@ivdc.chinacdc.cn
Received Date: 23 September 2023
Accepted Date: 04 December 2023
Available online: 07 December 2023

Abstract

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.
- Monkeypox virus (MPXV)
- , Metagenomic
- , Next generation sequencing
- , Amplicon
- , Third-generation sequencing

Electronic Supplementary Material

10.1016j.virs.2023.12.002-ESM.docx
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