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European pilot interlaboratory comparison study on Mpox virus whole genome sequencing

2025-09-22Journal article Open access
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dc.contributor.authorFuchs, Jonas
dc.contributor.authorBertelli, Claire
dc.contributor.authorPillonel, Trestan
dc.contributor.authorCordeiro, Rita
dc.contributor.authorIzopet, Jacques
dc.contributor.authorPasquier, Christophe
dc.contributor.authorLewandowski, Kuiama
dc.contributor.authorMaks, Anastasija
dc.contributor.authorMichel, Janine
dc.contributor.authorRodriguez-Sanchez, Belen
dc.contributor.authorSanches-Seco, Maria Paz
dc.contributor.authorLedesma, Juan
dc.contributor.authorSobral, Daniel
dc.contributor.authorVercauteren, Koen
dc.contributor.authorde Block, Tessa
dc.contributor.authorRezende, Antonio Mauro
dc.contributor.authorBrinkmann, Annika
dc.contributor.authorNitsche, Andreas
dc.contributor.authorGreub, Gilbert
dc.contributor.authorPanning, Marcus
dc.date.accessioned2025-12-04T15:33:43Z
dc.date.available2025-12-04T15:33:43Z
dc.date.issued2025-09-22
dc.description.abstractObjectives: Since 2022, distinct Mpox virus (MPXV) clades have been spreading across different geographic regions, causing a challenging epidemiological situation. Whole genome sequencing (WGS) proved to be instrumental for patient management and global public health. We report a pilot interlaboratory comparison study for MPXV WGS. Methods: We distributed noninfectious DNA samples, including the main MPXV clades I and II, to eight European laboratories. We included one cowpox (CPXV) sample as a specificity control. Participants were free to choose their WGS pipeline of choice to mimic a real-world scenario and were asked to report on the sequencing pipeline used, average genome coverage, and MPXV species, clade, and subclade assignments. Results: Seven of the eight invited laboratories reported results back. All participants largely identified the MPXV clades and reported high-quality genomes with minimal variations, specifically for MPXV clade IIb 2022 outbreak strains. However, reconstructed genomes showed high variability for nonclade IIb MPXV strains. The CPXV sample was correctly identified by three laboratories. Conclusions: Although results for MPXV clade IIb 2022 outbreak strains are reassuring, the inclusion of MPXV clade I and IIa strains highlights pitfalls for targeted sequencing approaches and subsequent bioinformatic analyses. Our findings underscore the need for standardized external quality assessment studies.eng
dc.description.sponsorshipThe European Society of Clinical Microbiology and Infectious Diseases study group on Genomic and Molecular Diagnostics (ESGMD) supported this study. Institute of Tropical Medicine Structurele Onderzoeksfinanciering (ITM's SOFI) programme supported by the Flemish Government, Science & Innovation cosupported this study. This study was cofunded by the European Union project “Sustainable use and integration of enhanced infrastructure into routine genome-based surveillance and outbreak investigation activities in Portugal”—GENEO (project number 101113460) on behalf of the EU4H programme (EU4H-2022-DGA-MS-IBA-01-02).
dc.identifier.citationClin Microbiol Infect. 2025 Sep 22:S1198-743X(25)00461-6. doi: 10.1016/j.cmi.2025.09.011. Online ahead of print
dc.identifier.doi10.1016/j.cmi.2025.09.011
dc.identifier.eissn1469-0691
dc.identifier.issn1198-743X
dc.identifier.pmid40992692
dc.identifier.urihttp://hdl.handle.net/10400.18/10638
dc.language.isoeng
dc.peerreviewedyes
dc.publisherElsevier
dc.relation101113460
dc.relation.hasversionhttps://www.clinicalmicrobiologyandinfection.org/article/S1198-743X(25)00461-6/fulltext
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectInterlaboratory Comparison Study
dc.subjectMpox Virus
dc.subjectPoxvirus
dc.subjectPrepardness
dc.subjectWhole Genome Sequencing
dc.subjectInfecções Sistémicas e Zoonoses
dc.titleEuropean pilot interlaboratory comparison study on Mpox virus whole genome sequencingeng
dc.typejournal article
dcterms.referenceshttps://www.clinicalmicrobiologyandinfection.org/cms/10.1016/j.cmi.2025.09.011/attachment/e0acefb8-f60c-4505-8ee3-f512b021ed3d/mmc1.pdf
dspace.entity.typePublication
oaire.citation.endPage00466
oaire.citation.startPageS1198-743X(25)00461-6
oaire.citation.titleClinical Microbiology and Infection
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85

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