Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison

Next-generation sequencing (NGS) is crucial for monitoring and investigating infectious disease outbreaks, providing essential data for public health decisions. The COVID-19 pandemic has significantly expanded pathogen sequencing and bioinformatics capacities worldwide, creating an opportunity to leverage these advancements for other pathogens with pandemic and epidemic potential. In response to the need for a systematic cost estimation approach for sustainable genomic surveillance, particularly in low- and middle-income countries, five institutions collaborated to develop the genomics costing tool (GCT). These institutions are the Association of Public Health Laboratories (APHL), FIND, The Global Fund to Fight AIDS, Tuberculosis and Malaria, the UK Health Security Agency (UKHSA), and the World Health Organization (WHO). To validate the GCT, it was piloted in public health laboratories across three WHO regions: African, Eastern Mediterranean, and European. The pilot exercises were intended to assess the tool’s accuracy, utility, and functionality, exploring scenarios for validating past expenditure, routine use, cost optimization, and scaling up sequencing services. Data from these pilots demonstrated significant cost reductions per sample with increased throughput, underscoring the economic benefits of the optimized use of sequencing platforms underpinned by sample throughput. The GCT enables laboratories to estimate and visualize costs, plan budgets, and improve cost-efficiencies for sequencing and bioinformatics based on factors such as equipment purchase and preventative maintenance, reagents and consumables, annual sample throughput, human resources training, quality assurance and management. This publication shares key findings from pilot exercises offering detailed insights into the cost of routine NGS implementation using either short- or long-read sequencing technologies, demonstrating the utility of GCT as an asset to support efforts for sustainable funding and strategic planning in genomic surveillance.