European pilot interlaboratory comparison study on mpox virus whole genome sequencing.

Abstract

Objectives: Since 2022, distinct mpox virus (MPXV) clades are 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 (ILC) study for MPXV WGS.

Methods: We distributed non-infectious DNA samples including the main MPXV clades I and II to eight European laboratories. We included one cowpox (CPXV) sample as 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 non-clade 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 assessement (EQA) studies.