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
  • [41] Proof of concept for multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer
    Whitford, Whitney
    Hawkins, Victoria
    Moodley, Kriebashne S.
    Grant, Matthew J.
    Lehnert, Klaus
    Snell, Russell G.
    Jacobsen, Jessie C.
    SCIENTIFIC REPORTS, 2022, 12 (01)
  • [42] Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification
    Franco-Sierra, Nicolas D.
    Diaz-Nieto, Juan F.
    ECOLOGY AND EVOLUTION, 2020, 10 (07): : 3544 - 3560
  • [43] First Draft Genome of the Trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore Technology and Illumina Sequencing
    d'Avila-Levy, Claudia M.
    Bearzatto, Bertrand
    Ambroise, Jerome
    Helaers, Raphael
    Butenko, Anzhelika
    Yurchenko, Vyacheslav
    Morelli, Karina A.
    Santos, Helena L. C.
    Brouillard, Pascal
    Grellier, Philippe
    Gala, Jean-Luc
    Vikkula, Miikka
    TROPICAL MEDICINE AND INFECTIOUS DISEASE, 2020, 5 (01)
  • [44] Global mpox lineage discovery and rapid outbreak tracking with nanopore sequencing
    Michael S. Bosmeny
    Adam A. White
    Adrian A. Pater
    Jennifer Crew
    Joshua Geltz
    Keith T. Gagnon
    Virology Journal, 20
  • [45] RespiCoV: Simultaneous identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and 46 respiratory tract viruses and bacteria by amplicon-based Oxford-Nanopore MinION sequencing
    Brinkmann, Annika
    Uddin, Steven
    Ulm, Sophie-Luisa
    Pape, Katharina
    Foerster, Sophie
    Enan, Khalid
    Nourlil, Jalal
    Krause, Eva
    Schaade, Lars
    Michel, Janine
    Nitsche, Andreas
    PLOS ONE, 2022, 17 (03):
  • [46] Global mpox lineage discovery and rapid outbreak tracking with nanopore sequencing
    Bosmeny, Michael S. S.
    White, Adam A. A.
    Pater, Adrian A. A.
    Crew, Jennifer
    Geltz, Joshua
    Gagnon, Keith T. T.
    VIROLOGY JOURNAL, 2023, 20 (01)
  • [47] Robust and sensitive amplicon-based whole-genome sequencing assay of respiratory syncytial virus subtype A and B
    Talts, Tiina
    Mosscrop, Lucy G.
    Williams, David
    Tregoning, John S.
    Paulo, Whitney
    Kohli, Arinder
    Williams, Thomas C.
    Hoschler, Katja
    Ellis, Joanna
    de Lusignan, Simon
    Zambon, Maria
    MICROBIOLOGY SPECTRUM, 2024, 12 (04):
  • [48] Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus
    Fitzpatrick, Amy H.
    Rupnik, Agnieszka
    O'Shea, Helen
    Crispie, Fiona
    Keaveney, Sinead
    Cotter, Paul D.
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2023, 89 (01)
  • [49] A rapid and affordable amplicon-based method for next-generation genome sequencing of the infectious bursal disease virus
    Techera, Claudia
    Tomas, Gonzalo
    Grecco, Sofia
    Williman, Joaquin
    Hernandez, Martin
    Olivera, Valeria
    Banda, Alejandro
    Vagnozzi, Ariel
    Panzera, Yanina
    Marandino, Ana
    Perez, Ruben
    JOURNAL OF VIROLOGICAL METHODS, 2023, 322
  • [50] A simplified, amplicon-based method for whole genome sequencing of human respiratory syncytial viruses
    Dong, Xiaomin
    Deng, Yi-Mo
    Aziz, Ammar
    Whitney, Paul
    Clark, Julia
    Harris, Patrick
    Bautista, Catherine
    Costa, Anna-Maria
    Waller, Gregory
    Daley, Andrew J.
    Wieringa, Megan
    Korman, Tony
    Barr, Ian G.
    JOURNAL OF CLINICAL VIROLOGY, 2023, 161
12345