Genome sequencing of the mpox virus 2022 outbreak with amplicon-based Oxford Nanopore MinION sequencing

被引：2
|
作者：
Brinkmann, Annika [1 ,2 ]
Pape, Katharina [1 ,2 ]
Uddin, Steven [1 ,2 ]
Woelk, Niklas [1 ,2 ]
Foerster, Sophie [1 ,2 ]
Jessen, Heiko [3 ]
Michel, Janine [1 ,2 ]
Kohl, Claudia [1 ,2 ]
Schaade, Lars [1 ,2 ]
Nitsche, Andreas [1 ,2 ]
机构：
[1] Robert Koch Inst, Ctr Biol Threats & Special Pathogens, WHO Reference Lab SARS CoV, Highly Pathogen Viruses, See str 10, D-13353 Berlin, Germany
[2] Robert Koch Inst, WHO Collaborating Ctr Emerging Infect & Biol Threa, German Consultant Lab Poxviruses, See str 10, D-13353 Berlin, Germany
[3] Praxis Jessen & Colleagues, Motz str 19, D-10777 Berlin, Germany
来源：
JOURNAL OF VIROLOGICAL METHODS | 2024年 / 325卷
关键词：
Orthopox viruses; Mpox virus; MinION; Nanopore sequencing; TO-HUMAN TRANSMISSION; MONKEYPOX;
D O I：
10.1016/j.jviromet.2024.114888
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
We present an amplicon-based assay for MinION Nanopore sequencing of mpox virus (MPXV) genomes from clinical specimens, obtaining high-quality results with an average genome coverage of 99% for Ct values of up to 25, and a genome coverage of 97.1% for Ct values from 25 to 30 which are challenging to sequence. This assay is easy to implement in PCR-based workflows and provides accurate genomic data within a short time.
引用
收藏
页数：4
相关论文
共 50 条
  • [1] Oxford Nanopore MinION Sequencing and Genome Assembly
    Hengyun Lu
    Francesca Giordano
    Zemin Ning
    Genomics,Proteomics & Bioinformatics, 2016, 14 (05) : 265 - 279
  • [2] Oxford Nanopore MinION Sequencing and Genome Assembly
    Lu, Hengyun
    Giordano, Francesca
    Ning, Zemin
    GENOMICS PROTEOMICS & BIOINFORMATICS, 2016, 14 (05) : 265 - 279
  • [3] Oxford Nanopore MinION Sequencing and Genome Assembly
    Hengyun Lu
    Francesca Giordano
    Zemin Ning
    Genomics,Proteomics & Bioinformatics, 2016, (05) : 265 - 279
  • [4] Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
    Andrea D. Tyler
    Laura Mataseje
    Chantel J. Urfano
    Lisa Schmidt
    Kym S. Antonation
    Michael R. Mulvey
    Cindi R. Corbett
    Scientific Reports, 8
  • [5] Evaluation of Oxford Nanopore's MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
    Tyler, Andrea D.
    Mataseje, Laura
    Urfano, Chantel J.
    Schmidt, Lisa
    Antonation, Kym S.
    Mulvey, Michael R.
    Corbett, Cindi R.
    SCIENTIFIC REPORTS, 2018, 8
  • [6] MinION nanopore sequencing of an influenza genome
    Wang, Jing
    Moore, Nicole E.
    Deng, Yi-Mo
    Eccles, David A.
    Hall, Richard J.
    FRONTIERS IN MICROBIOLOGY, 2015, 6
  • [7] Amplicon-Based Nanopore Sequencing of Hemoglobin Genes for Diagnosis of Thalassemia
    Wadsworth, P.
    Ho, C.
    Volkova, I.
    Edwards, C.
    Killinger, B.
    Suarez, C.
    JOURNAL OF MOLECULAR DIAGNOSTICS, 2024, 26 (11): : S5 - S5
  • [8] Molecular diagnosis of patients with hepatitis A virus infection using amplicon-based nanopore sequencing
    Lee, Geum-Young
    Park, Kyungmin
    Lee, Young-Sun
    Kim, Ji Hoon
    Byun, Kwan Soo
    Kim, Jongwoo
    Kim, Won-Keun
    Song, Jin-Won
    PLOS ONE, 2023, 18 (07):
  • [9] The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
    Miten Jain
    Hugh E. Olsen
    Benedict Paten
    Mark Akeson
    Genome Biology, 17
  • [10] The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
    Jain, Miten
    Olsen, Hugh E.
    Paten, Benedict
    Akeson, Mark
    GENOME BIOLOGY, 2016, 17
12345