WHO and partners launch updated Genomics Costing Tool to help in planning sustainable genomic surveillance

WHO in collaboration with the Association of Public Health Laboratories (APHL), FIND and the United Kingdom Health Security Agency (UKHSA) have released an updated version of their Genomics Costing Tool (GCT 2.0), designed to help countries understand how much it costs to set up, scale up and run genomic surveillance systems - and how to do so sustainably.

Genomic surveillance helps countries track pathogens by analysing their biological "fingerprints". This makes it possible to detect outbreaks earlier, monitor how diseases spread and respond more effectively. However, building and maintaining these systems can be complex and expensive. The updated tool helps countries plan these investments in a clear and practical way.

Commenting on the launch of the new edition of the tool, Dr Joanna Salvi Le Garrec, Technical Officer at WHO/Europe and Lead on the Better Labs for Better Health initiative said: "Genomic surveillance is becoming an essential part of public health, both in our region and globally, but its sustainability depends on understanding the true cost of the full workflow, which can be considerable. By making these costs more visible and structured, the updated tool supports more cost-efficient planning and helps ensure that genomic surveillance is not only implemented but maintained over time".

From COVID-19 to broader public health impact

The first edition of the tool was developed during the COVID-19 pandemic, when countries urgently needed to estimate the costs of testing the genetic makeup of the virus that causes COVID-19 (SARS-CoV-2). Over the past 6 months alone, it has been downloaded more than 390 times, reflecting strong global demand for practical planning tools.

However, feedback from users highlighted an important gap: countries wanted to apply the same approach to other priority diseases. At the same time, WHO's "Global genomic surveillance strategy for pathogens with pandemic and epidemic potential, 2022-2032" calls for integrating genetic analysis of viruses and bacteria into everyday disease monitoring systems, not just SARS-CoV-2.

The second edition was developed in response to this need.

What difference will the new tool make?

The updated tool allows countries to estimate costs not just for SARS-CoV-2, but for a wider range of pathogens, including influenza viruses and tuberculosis. This means countries can now:

• plan long-term investments, rather than short-term emergency responses;
• compare different approaches, such as different technologies or ways of testing samples, to find the most cost-effective option;
• understand the full cost picture, including equipment, staff, consumables and systems to ensure reliable and accurate results; and
• scale up gradually, based on available resources and national priorities.

By making costs more transparent, the tool supports better decision-making and helps governments and partners invest where it matters most.

Designed for real-world use

The launch of the global Genomics Costing Tool comes after the successful piloting of a similar tool in Georgia, Kosovo, Kyrgyzstan, Republic of Moldova and Uzbekistan in 2019, under the Better Labs for Better Health initiative.

Using lessons learned from this pilot, the Genomics Costing Tool provides a simple, interactive Excel-based resource that guides users step by step and can be adapted to different country contexts.

It is intended for a wide range of users, including policy-makers, laboratory leaders, health programme managers and funding partners - anyone involved in planning or supporting genomic surveillance.

The tool is accompanied by a user manual that explains how to collect data, estimate costs and interpret results to inform decisions.

The tool is available in English, French, Russian and Spanish. The user manual is currently available in English, with additional languages to follow. Users can request support via [email protected], and training materials will be released in the coming months.

Supporting stronger, more resilient health systems

As countries continue to integrate genetic testing of viruses and bacteria into routine disease monitoring and outbreak response, having a clear understanding of costs is essential.

By helping countries plan smarter and invest more effectively, the Genomics Costing Tool contributes to building stronger, more resilient health systems - better prepared to detect and respond to current and future health threats.

WHO working in partnership to improve genetic surveillance systems

The following organizations gratefully acknowledge the financial contributions that supported the development and publication of this tool:

• APHL was supported by the United States Centers for Disease Control and Prevention.
• FIND was supported by Unitaid and the Netherlands Enterprise Agency.
• WHO was supported by the Australian Department of Foreign Affairs and Trade and the International Pathogen Surveillance Network (WHO Hub for Pandemic and Epidemic Intelligence).

Commenting on the development of the tool, Dr Marco Marklewitz from FIND's genomics and sequencing department said: "This has been a truly collaborative effort, bringing together partners and experts from across disciplines around a shared goal. The resulting tool reflects that collective commitment, and we hope it will support laboratories and the broader public health community in strengthening genomic surveillance systems".