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

Annika Brinkmann; Katharina Pape; Steven Uddin; Niklas Woelk; Sophie Förster; Heiko Jessen; Janine Michel; Claudia Kohl; Lars Schaade; Andreas Nitsche

doi:10.1016/j.jviromet.2024.114888

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

J Virol Methods. 2024 Apr:325:114888. doi: 10.1016/j.jviromet.2024.114888. Epub 2024 Jan 20.

Authors

Affiliations

¹ Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany. Electronic address: BrinkmannA@rki.de.
² Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany.
³ Praxis Jessen and Colleagues, Motzstraße 19, 10777 Berlin, Germany.

PMID: 38246565
DOI: 10.1016/j.jviromet.2024.114888

Abstract

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.

Keywords: MinION; Mpox virus; Nanopore sequencing; Orthopox viruses.

MeSH terms

Genomics
High-Throughput Nucleotide Sequencing / methods
Monkeypox virus
Nanopore Sequencing*
Nanopores*