Development and validation of a new mpox virus sequencing and bioinformatic analysis pipeline
Sequencing and bioinformatic analysis of mpox virus (MPXV) remain challenging in resource-limited settings. We developed and validated a PCR-based sequencing assay that targets a 12.5 kilobase (kb) region that is phylogenetically representative of the whole ∼ 200 kb MPXV genome. We combined this sequencing assay with a lightweight, downloadable, on-and-off-grid-bioinformatics pipeline for rapid phylogenetic analysis. Our findings demonstrate that this simplified sequencing method, and the associated bioinformatics pipeline accurately distinguished clades, subclades, and clusters of MPXV. Therefore, this assay will provide rapid sequence information for understanding transmission patterns and sources of outbreaks in resource-limited settings. In addition, this assay provides a unique opportunity to decentralize mpox molecular surveillance capacities that are needed to contain the ongoing outbreak.
Authors
- Claude Kwe Yinda (ORCID: https://orcid.org/0000-0002-5195-5478)
- Félix Koukouikila-Koussounda (ORCID: https://orcid.org/0009-0006-6543-0839)
- Skyler A. Kuhn (ORCID: https://orcid.org/0000-0003-0606-2125)
- Vincent J. Munster (ORCID: https://orcid.org/0000-0002-2288-3196)
- Missiani Ochwoto (ORCID: https://orcid.org/0000-0001-7143-7283)
- Jonathan E. Schulz (ORCID: https://orcid.org/0000-0001-5462-5952)
- Justin Lack (ORCID: https://orcid.org/0000-0003-0584-4010)
- Craig Martens (ORCID: https://orcid.org/0000-0001-8112-2234)
- Paul Schaughency (ORCID: https://orcid.org/0000-0002-3358-2102)
- Ryan F. Relich (ORCID: https://orcid.org/0000-0001-5889-1190)
- Ben Greene
- Dachel Aymard Eyenet Boussam
- Fabien Roch Niama
- Reiche Golmard Elenga (ORCID: https://orcid.org/0009-0005-2684-4273)
- Kailin Hawes
- Pembe Issamou Mayangue
Institutions
- National Institutes of Health (US)
- Laboratoire National de Santé Publique du Congo (CG)
- National Institute of Allergy and Infectious Diseases (US)
- Laboratoire National de Santé (LU)
- University School (US)
- Indiana University School of Medicine
- Indiana University (US)
- Marien Ngouabi University (CG)
Publication Details
- Journal
- Emerging Microbes & Infections
- Published
- 2025-04-15
- DOI
- https://doi.org/10.1080/22221751.2025.2494733
- Citations
- 3
- Primary Topic
- Poxvirus research and outbreaks
- Type
- article
- Field-Weighted Citation Impact
- 3.11
Funders
- National Institutes of Health
- National Institute of Allergy and Infectious Diseases