Lab Matters Winter 2025 | Page 21

GLOBAL HEALTH

By Ashley Bolding, specialist, Global Health

The COVID-19 pandemic accelerated the global adoption of next generation sequencing( NGS) and highlighted the need for sustainable financial planning in genomic surveillance. During the pandemic, international donors and governments increased investments in sequencing infrastructure and workforce development to strengthen SARS-CoV-2 genomic surveillance. While this surge in investment allowed countries to build capacity rapidly, it also revealed a structural challenge: much of the financing was short-term, reactive and tied to the emergency response. As the immediate crisis subsides, maintaining these systems requires new approaches that ensure laboratories can sustain NGS activities beyond a single pathogen focus. Without long-term investment and financial planning, there is a significant risk of losing both the technological gains and the skilled workforce developed during the pandemic.

The Genomics Costing Tool

APHL, FIND, The Global Fund to Fight AIDS, Tuberculosis and Malaria, the United Kingdom Health Security Agency( UKHSA), the International Pathogen Surveillance Network and the World Health Organization( WHO) formed a working group to develop a comprehensive Genomics Costing Tool( GCT) to support systematic costing for sustainable genomic surveillance. The GCT, an Excel-based tool, was first developed for SARS-CoV-2 sequencing. It enables users to calculate total sequencing costs, including reagents, consumables, equipment, human resources, facilities, transportation, bioinformatics and quality management, with results calculated by sample, year, cost category or workflow step. The tool is intended for a wide range of partners, including policymakers, laboratory personnel, procurement and quality managers, health administrators, economists and donor institutions. In 2023, the GCT was piloted and validated in countries within three WHO regions— Africa, Eastern Mediterranean and Europe— to assess accuracy, utility and functionality in diverse laboratory settings.

Looking Forward to GCT 2.0

Feedback from these pilots highlighted the importance of expanding the tool’ s scope. A global landscape analysis survey was conducted to assess the diverse needs and utilization of NGS, informing priorities for a new GCT. Respondents emphasized that NGS is now utilized or hoped to be utilized for a wide range of public health priorities, including influenza surveillance, antimicrobial resistance monitoring, foodborne pathogens, vector-borne diseases such as malaria and dengue, and emerging threats like mpox and Ebola viruses. The expansion beyond SARS-CoV-2 requires costing approaches that account for different throughput levels, diverse platforms and pathogen-specific workflows.

In response, a second edition of the GCT is in development to accommodate these expanded requirements. The updated tool will include compatibility with individualized annual throughput capacities, customizable laboratory workflows and support for additional sequencing platforms and pathogens. These enhancements reflect both the evolving needs of global public health systems and the technological diversification of NGS. By providing flexibility across surveillance contexts, the new GCT will expand its relevance for low- and middle-income countries where budgeting constraints are particularly acute and will enable laboratories and policymakers to generate comprehensive financial insights, identify cost-efficiencies and align resources strategically across both sequencing and bioinformatic processes. The second edition is expected to be published by WHO early in 2026.

Ultimately, the development of a second GCT edition underscored a broader

Members of the Genomics Costing Tool Working Group

APHL Noah Hull Angela Poates Ashley Bolding Jessica Rowland Toni Whistler

WHO Joanna Salvi Le Garrec Zwetyenga Oluwatosin Wuraola Akande Alexandr Jaguparov Biran Musul Josefina Campos Aude Wilhelm Silvia Argimon Soudeh Ehsani Sophia Georghiou Dmitriy Pereyaslov

UKHSA Babak Afrough Beatrix Kele Aude Wilhelm

FIND Marco Marklewitz Anita Suresh Swapna Uplekar Miguel Moreno-Molina

principle: pandemic-driven investments must transition into sustainable, routine systems that serve multiple public health purposes. The global acceptance of NGS created an unprecedented opportunity to integrate genomics into routine surveillance, but progress will only be lasting if supported by consistent funding, skilled workforce development, appropriate use of equipment and infrastructure maintenance. By equipping participants with reliable costing data, the GCT provides a critical foundation for cost-efficient long-term planning, helping ensure that the gains made during COVID-19 translate into resilient, multipurpose genomic surveillance systems capable of addressing both current and future health threats. g