From surveillance to systems: Scaling environmental genomics for epidemic preparedness in Africa

Learn about ODIN-Mpox, a project focusing on the rapid detection and monitoring of Mpox, alongside other waterborne pathogens, to improve epidemic preparedness by embedding innovative technologies into national health infrastructures

Zoonotic outbreaks are increasing in frequency and complexity, exposing persistent gaps in early detection systems. The recent Mpox emergency in Africa highlighted the limitations of traditional surveillance approaches. Environmental surveillance, combining wastewater monitoring with genomic sequencing, is now moving from concept to implementation. Through the Horizon Europe-funded ODIN and ODIN-Mpox initiatives, this approach is being operationalised across Africa, demonstrating how integrated, field-ready systems can strengthen preparedness and enable earlier public health responses.

The importance of epidemic preparedness

Mpox has re-emerged as a major public health threat in Central Africa, with outbreaks in the Democratic Republic of Congo prompting emergency declarations at national, continental, and global levels. Yet detection continues to rely heavily on clinical surveillance systems that are often fragmented, resource-constrained, and limited in reach, particularly in underserved areas.

Environmental surveillance has already proven its value globally, from poliovirus monitoring to SARS-CoV-2 wastewater tracking, by capturing pathogen signals from entire populations, including asymptomatic individuals. Through Horizon Europe and the Global Health EDCTP3 programme, the European Union has supported initiatives such as ODIN and ODIN-Mpox to strengthen Africa’s capacity for genomic surveillance and support sustainable, locally led surveillance systems within national public health infrastructures.

From concept to deployment: ODIN-Mpox in action

Project ODIN and its complementary initiative, ODIN-Mpox, are advancing environmental surveillance across Burkina Faso, the Democratic Republic of Congo, and Tanzania, with planned expansion into additional countries. Together, they focus on monitoring waterborne pathogens including Vibrio cholerae, Salmonella Typhi, poliovirus, and emerging threats such as Mpox. ⁽¹⁾

ODIN-Mpox builds directly on the same consortium, leadership, and technological foundation established by ODIN. While maintaining a shared surveillance platform, ODIN-Mpox specifically targets the rapid detection and monitoring of Mpox, demonstrating how the system can be adapted rapidly to emerging public health threats.

A key innovation is the deployment of Laboratories on Wheels (LoW), mobile laboratories capable of conducting genomic sequencing and qPCR analyses directly in the field. These units enable surveillance in non-sewered environments such as informal settlements and rural communities, where traditional wastewater systems are absent. ⁽²⁾

Recent deployment activities in Tanzania demonstrated the feasibility of this approach, generating over 70 environmental metagenomes and confirming the presence of Mpox through targeted sequencing.

Standardised protocols, published as open-access SOPs, ensure harmonised implementation across countries. In parallel, the project has developed a bioinformatics infrastructure and analytical pipeline deployable in both mobile and static laboratories, enabling near real-time interpretation of results.

Building sustainable surveillance systems

A defining feature of ODIN and ODIN-Mpox is their emphasis on long-term capacity building and system ownership. Across participating countries, more than 75 researchers have received hands-on training in genomic surveillance, covering workflows from sample collection to sequencing and bioinformatics analysis. The project also supports three MSc students in bioinformatics, contributing to a sustainable workforce pipeline.

Training programmes in Tanzania strengthened national public health laboratories’ ability to detect, analyse, and respond to pathogens and antimicrobial resistance in wastewater. These efforts are complemented by the development of national knowledge hubs and communities of practice designed to support real-time analytics and evidence-based decision-making.

Beyond national capacity building, ODIN-Mpox is contributing to regional and global knowledge exchange. A recent global webinar attracted participants from more than 60 countries, highlighting growing interest in scalable environmental surveillance solutions.

The project is also contributing directly to development of the Africa CDC Continental Wastewater and Environmental Surveillance Strategy (2026–2031), positioning environmental genomics as a cornerstone of future public health systems.

Policy relevance: From innovation to infrastructure

Environmental surveillance offers an important early warning capability, enabling detection of pathogens before clinical cases are widely reported. In the case of Mpox, this provides critical time for targeted interventions, including vaccination campaigns and outbreak containment measures.

By deploying mobile laboratories and adapting protocols to non-sewered environments, ODIN-Mpox ensures that surveillance reaches populations often excluded from traditional systems. This aligns with the One Health framework, recognising the interconnectedness of human, animal, and environmental health.

The initiative aligns with the WHO Pandemic Agreement, the EU Global Health Strategy, and the Africa CDC Pathogen Genomics Initiative. However, regulatory barriers, limited infrastructure, and gaps in clinical data integration continue to hinder implementation, requiring sustained investment and stronger governance frameworks.

ODIN-Mpox demonstrates that environmental surveillance is not merely an innovation but a foundational component of resilient health systems.

Next steps and call to action

The next phase of ODIN-Mpox focuses on expanding surveillance activities to additional countries, including Malawi and Ethiopia, while strengthening integration with national and regional health systems. Continued investment in training, mobile laboratory deployment, and advanced bioinformatics will be essential to sustain and scale these efforts.

To fully realise the potential of environmental surveillance, policymakers and global health stakeholders must act decisively. We call for:

• Recognition of environmental surveillance as core public health infrastructure embedded within preparedness and response strategies.
• Integration of genomic wastewater surveillance with clinical systems for real-time monitoring of disease dynamics.
• Sustained funding for laboratory networks, workforce development, and data systems.

The ODIN and ODIN-Mpox initiatives demonstrate how environmental genomics can shift public health from reactive response to proactive prevention, enabling earlier outbreak detection and more resilient health systems.

References

1. Lood R, Maketa VT, Kingpriest P. Environmental surveillance as a sentinel for emerging outbreaks: Lessons from mpox in Africa. Open Access Government. 2026 Jan 15;49(1):34–5. doi:10.56367/OAG-049-12345
2. Krolicka A, Thanh Tam Toan T, Shea D, Le Tressoler A, Bagi A, Okoli AS, et al. Human pathogen surveillance using a mobile and semi-autonomous environmental workflow Zenodo. doi:10.5281/ZENODO.14209149