European pilot interlaboratory comparison study on Mpox virus whole genome sequencing

Area of Science:

• Virology
• Genomic Epidemiology
• Public Health Microbiology

Background:

• Distinct Mpox virus (MPXV) clades have emerged globally since 2022, complicating epidemiological tracking.
• Whole genome sequencing (WGS) is crucial for patient management and monitoring MPXV spread.
• An interlaboratory comparison study was designed to assess MPXV WGS performance.

Purpose of the Study:

• To evaluate the performance of different laboratories in whole genome sequencing of Mpox virus.
• To identify potential challenges and areas for improvement in MPXV genomic surveillance.
• To assess the accuracy of clade and subclade identification for various MPXV strains.

Main Methods:

• Noninfectious DNA samples of MPXV clades I and II, and a cowpox virus (CPXV) control, were distributed to eight European laboratories.
• Participating labs utilized their preferred WGS pipelines, mimicking real-world conditions.
• Data reported included sequencing pipeline, genome coverage, and MPXV/CPXV identification.

Main Results:

• Seven laboratories submitted results, largely identifying MPXV clades accurately.
• High-quality genomes with minimal variations were reported for MPXV clade IIb 2022 strains.
• Significant variability was observed in genome reconstruction for non-clade IIb MPXV strains; CPXV was correctly identified by three labs.

Conclusions:

• While MPXV clade IIb 2022 strain sequencing is reliable, challenges remain for MPXV clades I and IIa.
• Targeted sequencing and bioinformatics analysis present potential pitfalls for certain MPXV clades.
• Standardized external quality assessment studies are essential for robust MPXV genomic surveillance.