Marklewitz Marco, Jaguparov Alexandr, Wilhelm Aude, Akande Oluwatosin Wuraola, Musul Biran, Poates Angela Lee, Afrough Babak, Norberg Ashley, Hull Noah Clayton, Ehsani Soudeh, Salvi Le Garrec Joanna, Whistler Toni
FIND, Geneva, Switzerland.
Infectious Hazard Management, World Health Organization Regional Office for Europe, Copenhagen, Denmark.
Front Public Health. 2025 Jan 15;12:1498094. doi: 10.3389/fpubh.2024.1498094. eCollection 2024.
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.
下一代测序（NGS）对于监测和调查传染病爆发至关重要，可为公共卫生决策提供重要数据。新冠疫情在全球范围内显著扩大了病原体测序和生物信息学能力，为利用这些进展应对其他具有大流行和流行潜力的病原体创造了机会。为满足特别是低收入和中等收入国家对可持续基因组监测进行系统成本估算方法的需求，五个机构合作开发了基因组成本核算工具（GCT）。这些机构分别是公共卫生实验室协会（APHL）、FIND、抗击艾滋病、结核病和疟疾全球基金、英国卫生安全局（UKHSA）以及世界卫生组织（WHO）。为验证GCT，在WHO的三个区域（非洲、东地中海和欧洲）的公共卫生实验室进行了试点。试点旨在评估该工具的准确性、实用性和功能，探索验证过去支出、常规使用、成本优化以及扩大测序服务规模的方案。这些试点的数据表明，随着通量增加，每个样本的成本显著降低，凸显了基于样本通量优化使用测序平台的经济效益。GCT使实验室能够根据设备采购和预防性维护、试剂和耗材、年度样本通量、人力资源培训、质量保证和管理等因素，估算和可视化成本、规划预算并提高测序和生物信息学的成本效益。本出版物分享了试点的关键发现，深入详细地洞察了使用短读长或长读长测序技术进行常规NGS实施的成本，证明了GCT作为一种资产的效用，有助于支持基因组监测中的可持续资金筹集和战略规划工作。
