Skip to main content

ORIGINAL RESEARCH article

Front. Public Health
Sec. Infectious Diseases: Epidemiology and Prevention
Volume 12 - 2024 | doi: 10.3389/fpubh.2024.1498094

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

Provisionally accepted
Marco Marklewitz Marco Marklewitz 1Alexandr Jaguparov Alexandr Jaguparov 2Aude Wilhelm Aude Wilhelm 3Oluwatosin Wuraola Akande Oluwatosin Wuraola Akande 4*Biran Musul Biran Musul 5Angela Poates Angela Poates 6Babak Afrough Babak Afrough 3Ashley Norberg Ashley Norberg 6Noah C. Hull Noah C. Hull 6Soudeh Ehsani Soudeh Ehsani 2Joanna Salvi Le Garrec Joanna Salvi Le Garrec 2Toni Whistler Toni Whistler 7Anita Suresh Anita Suresh 1Beatrix Kele Beatrix Kele 3Bright Adu Bright Adu 8Christopher Sunkwa Tamal Christopher Sunkwa Tamal 9Gifty Boateng Gifty Boateng 10Gulmira Kalmambetova Gulmira Kalmambetova 11Hanan Al Kindi Hanan Al Kindi 12Kwame Asante Kwame Asante 13Leena Inamdar Leena Inamdar 3Nicksy Hieronyma Nelisiwe Gumede Nicksy Hieronyma Nelisiwe Gumede 14Swapna Uplekar Swapna Uplekar 1Yathrib Al Zakwani Yathrib Al Zakwani 12
  • 1 Foundation for Innovative New Diagnostics, Geneva, Geneva, Switzerland
  • 2 World Health Organization Regional Office for Europe, Copenhagen, Denmark
  • 3 UK Health Security Agency (UKHSA), London, United Kingdom
  • 4 World Health Organization (Switzerland), Geneva, Switzerland
  • 5 World Health Organization (Turkey), Ankara, Ankara, Türkiye
  • 6 Association of Public Health Laboratories, Silver Spring, Maryland, United States
  • 7 Global Fund to Fight AIDS, Tuberculosis and Malaria, Vernier, Switzerland
  • 8 Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
  • 9 World Health Organization (Ghana), Accra, Ghana
  • 10 Ghana Health Service, Accra, Ghana
  • 11 National TB Reference Laboratory, Bishkek, Kyrgyzstan
  • 12 Centre for Disease Control and Prevention, Ministry of Health, Muscat, Oman
  • 13 Association of Public Health Laboratories, Accra, Ghana
  • 14 World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo

The final, formatted version of the article will be published soon.

    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 (UK HSA), 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 of sequencing services. Data from these pilots demonstrated significant cost reductions per sample with increased throughput, underscoring the economic benefits of the optimizsed use of sequencing platforms underpinned by sample throughput.The GCT enables laboratories to estimate and visualize costs, plan budgets, and improve costefficiencies 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-read 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.

    Keywords: Next-generation sequencing, costing tool, COVID-19, cost-analysis, Genomic surveillance

    Received: 19 Sep 2024; Accepted: 19 Dec 2024.

    Copyright: © 2024 Marklewitz, Jaguparov, Wilhelm, Akande, Musul, Poates, Afrough, Norberg, Hull, Ehsani, Salvi Le Garrec, Whistler, Suresh, Kele, Adu, Tamal, Boateng, Kalmambetova, Al Kindi, Asante, Inamdar, Gumede, Uplekar and Al Zakwani. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Oluwatosin Wuraola Akande, World Health Organization (Switzerland), Geneva, Switzerland

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.