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Driver Project

Mpox

Genomic analysis of Mpox virus (MPXV) is a critical component of global outbreak response and surveillance. Public health laboratories face challenges in adopting and integrating appropriate bioinformatics tools to support sequencing, analysis, and data sharing. To address this, the PHA4GE Bioinformatics Pipelines and Visualization Working Group has developed a living resource that identifies key challenges in MPXV genomic analysis and highlights open-access, community-supported bioinformatics solutions.

Problem Statement

Although sequencing capacity for Mpox has expanded rapidly during outbreaks, laboratories encounter obstacles in generating consensus assemblies, standardising metadata for sequence submissions, detecting and interpreting variants of concern, and performing phylogenetic analyses. Available tools are dispersed across platforms, often lack Mpox-specific optimisation, and are inconsistently documented. Without accessible, harmonised guidance, public health teams risk delays in data processing and reduced ability to translate genomic findings into actionable insights.

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Working Groups

Implementation Framework

PHA4GE, through its Bioinformatics Pipelines and Visualization Working Group, is coordinating efforts to:

Define Bioinformatics Challenges

Curate Open-Access Solutions

Promote Community Engagement

Connect to Public Data

By consolidating best practices and openly available resources, this initiative aims to lower barriers for laboratories worldwide, enabling consistent, timely, and effective use of Mpox genomic data in public health decision-making.

Read Guidance Document

Resources

MPox Contextual Data Specification

The MPox Contextual Data Specification is an ontology-based, FAIR-aligned framework designed to standardize metadata collection for mpox genomic surveillance. Implemented through the DataHarmonizer platform, the package includes structured collection templates, field and term reference guides, and curation and new term request SOPs to support consistent, interoperable data sharing. Supporting both Canadian and international use cases, the specification enhances data quality, comparability, and collaborative pathogen surveillance across laboratories and public health agencies.

The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance

During the 2022 and 2024 global Mpox outbreaks, a standardized contextual data specification was developed to support public health genomic surveillance of MPXV. The specification defines ontology-based fields and controlled vocabularies for harmonized capture of sample metadata, epidemiological, clinical, laboratory, and methodological information, with emphasis on geo-temporal context, data provenance, and sampling strategy. Implemented within the open-source DataHarmonizer platform, the MPXV specification enables structured curation, validation, and transformation of surveillance data and is currently in use in Canada, with international applicability and extensibility to other pathogens.

Bioinformatics Solutions for Mpox Genomic Analysis

PHA4GE provides a community-driven, living guidance document for MPXV genomic analysis, identifying key challenges and open-source bioinformatics tools for public health use. The resource supports ongoing collaboration and updates as methods and tools evolve.

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