Next-generation sequencing and bioinformatics capacity: findings from a multi-country survey to guide the genomics...

Next-generation sequencing (NGS) and bioinformatics are critical to infectious disease surveillance, outbreak detection and response, and the research and development of medical countermeasures. Achieving sustainable genomic surveillance requires countries to develop costed national strategies that integrate financial planning and budgeting across sequencing and bioinformatics activities. The genomics costing tool (GCT) was initially developed to estimate the costs of SARS-CoV-2 sequencing and associated bioinformatics. In response to growing country demand, the tool has now been expanded to support a wider range of pathogens and laboratory settings (GCT 2.0). To inform the design of GCT 2.0, a cross-sectional online survey was disseminated between September 2024 and March 2025 to assess current global next-generation sequencing and bioinformatics capacity. Respondents were recruited via professional networks, mailing lists, and partner organizations. The questionnaire captured laboratory demographics, instrumentation, reagents, throughput, data management, bioinformatics/analytical tools, and funding sources. Of the 149 respondents, 120 responses from 52 countries across all six WHO regions were included in the analysis, after excluding incomplete submissions. The median number of sequencing instruments per respondent was 3, with Illumina and Oxford Nanopore Technologies being the most predominant platforms, reported by 89.6 and 68.8% of the respondents, respectively. The median annual throughput reported was 1,940 samples in high-income countries, 850 in upper-middle-income countries, 1,205 in lower-middle-income countries, and 950 in low-income countries. Only 57.7% of respondents stored data in multiple locations, and 32.5% lacked any data backup. Funding sources varied: 54.4% relied on multiple streams, while 14.9% depended solely on government budgets, and many laboratories relied on emergency or project-based support. Global NGS and bioinformatics capacity continues to expand, yet substantial geographical and operational disparities persist. Beyond instrument availability, laboratories face constraints related to throughput, data storage, analysis capacity, and sustainable financing. Informed by these findings, GCT 2.0 incorporates expanded pathogen coverage, flexible throughput scenarios, support for multiple sequencing platforms, and detailed costing of data storage and bioinformatics workflows. By integrating these considerations, the tool aims to strengthen laboratories' capacity to plan, manage, and sustain genomic surveillance over the long term.