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

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...

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Bibliographic Details
Published in:Journal of virological methods 2024-04, Vol.325, p.114888, Article 114888
Main Authors: Brinkmann, Annika, Pape, Katharina, Uddin, Steven, Woelk, Niklas, Förster, Sophie, Jessen, Heiko, Michel, Janine, Kohl, Claudia, Schaade, Lars, Nitsche, Andreas
Format: Article
Language:English
Subjects:
Genomics
High-Throughput Nucleotide Sequencing - methods
MinION
Monkeypox virus
Mpox (monkeypox)
Mpox virus
Nanopore Sequencing
Nanopores
Orthopox viruses
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Summary: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. •We present an amplicon-based assay for MinION Nanopore sequencing of MPXV genomes from clinical specimens•High-quality results with full coverage of the genomes, even for samples with high Ct values of up to 30 can be obtained•Only 200,000 reads are necessary for full coverage of the genome
ISSN:0166-0934
1879-0984
1879-0984
DOI:10.1016/j.jviromet.2024.114888