Integrating Genomic and Modelling Insights into Routine IDSR: A Qualitative Study Protocol to Strengthen Outbreak Response in East and Central Africa

<ns5:p> Background Populations across Africa remain at risk of catastrophic impacts of novel disease outbreaks, including those with pandemic potential, reflecting vulnerability in public health infrastructure and response capacity. Despite notable advancements in outbreak response, integrated approaches that translate genomic and modelling data into actionable public health interventions remain underutilised in Africa. Emerging outbreak investigation frameworks that incorporate genomic and modelling data are often insufficiently embedded within national health systems, limiting their contribution to inform public health decision-making <ns5:bold>.</ns5:bold> To address these gaps, this study is being conducted as part of a larger NIHR-funded Global Health Research Group on Virus genomics and outbreak (ViGOR) project <ns5:bold>.</ns5:bold> Methods This study will be conducted in three countries: Kenya, Democratic Republic of Congo (DRC), and the Union of the Comoros. Utilising a qualitative mixed-methods research approach grounded in Participatory Action Research (PAR), we will conduct a series of investigations outlined below: (i) undertake stakeholder and community engagement to build awareness on the use of genomic and modelling data in outbreak investigation; (ii) conduct focused group discussions (FGDs) with community representatives to explore perceptions on genomics and disease modelling in disease outbreak response and identify social, ethical, and contextual facilitators and barriers; (iii) conduct Key Informant Interviews (KIIs) with front-line disease surveillance and response teams, to elicit views on integrating genomic and modelling data into routine outbreak control; (iv) Organise policy dialogues to develop a framework for applying these data in routine integrated disease surveillance and response (IDSR) activities; and (v) undertake costing analysis from a provider perspective, combining both ingredients-based and top-down costing approaches, to estimate the direct costs of generating genomic and modelling data and implementing the framework. Expected Findings The study is expected to generate actionable insights to facilitate integration of genomic and modelling data into routine IDSR systems across the three countries. Through sustained stakeholder engagement, it will strengthen partnerships among researchers, policymakers, and communities, enhancing real-time use of genomic and modelling evidence in outbreak surveillance and response, support timely outbreak management and sustainable health system strengthening. </ns5:p>