During outbreaks of Ebola, influenza, or measles in East and Central Africa, public health officials often lack the genomic data needed to track how the virus is spreading and which interventions will work best. The ViGOR project builds a permanent pipeline that links virus genome sequencing directly into national outbreak response systems across Kenya, the Democratic Republic of Congo, and Comoros. At present, genomic insights from outbreaks are generated but rarely feed into real-time policy decisions. This project embeds laboratory protocols, bioinformatic analysis, and high-performance computing within three partner reference laboratories that already work with their countries’ ministries of health. If successful, ViGOR will give local health authorities the ability to sequence outbreak samples, identify transmission chains, and evaluate control measures within days rather than months. The project also develops open-access methods for a range of viruses—Ebola, influenza, SARS-CoV-2, rotavirus, measles, and dengue—and trains local researchers through bespoke courses and fellowships. The result is not a single study but a durable infrastructure: a template for how reference laboratories across Africa can routinely generate policy-relevant genomic data during viral outbreaks.
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Identifying effective and proportionate public health control measures for infectious disease outbreaks relies on detailed data about the pathogen, its distribution, and its transmission. This project will show how genomic investigation coupled to outbreak surveillance and modern quantitative epidemiological approaches can provide much of this information, allowing refinement of interventions in LMIC settings. Virus genomics has played a key role in recent disease outbreaks including Ebola, Zika, and the H1N1 influenza and SARS-CoV-2 pandemics. However, genomic investigation and public health policy are not always closely linked, and genomic insights are often underused. To redress this issue requires an integrated pipeline of laboratory and computational protocols embedded within public health systems, from rapid diagnostic capacity to the ability to evaluate potential intervention strategies. This integrated use of genomics could revolutionise public health in African LMICs if the skills and resources are made available. The ViGOR project addresses this missed opportunity through a collaboration between the University of Warwick, renowned for infectious disease epidemiology, and KEMRI-Wellcome Trust Research Programme in Kenya, a regional genomics centre. This expertise will be exported through three Partner reference laboratories in Kenya, the Democratic Republic of Congo, and Comoros, each of which plays a pivotal role in national outbreak surveillance. We will support and enhance their genomics technical development and infrastructure, bioinformatic analysis and high-performance computing to enable a comprehensive integrated response to virus outbreak threats. The project aims to reshape public health in the region through the deployment and dissemination of genomic and bioinformatic tools. We will develop off-the-shelf open access genomics sequencing and analysis methods for a range of outbreak virus pathogens, including Ebola, influenza, SARS-CoV-2, rotavirus, measles and dengue. This knowledge will be established within three Partner laboratories providing the necessary virus genomic methods and associated expertise to generate policy-relevant scientific reports. Using this new capability to sequence and analyse archived outbreak samples we will advance our understanding of virus outbreaks (globally and in the region). These methods will be applied prospectively to new viral threats that arise during the project, helping to determine appropriate interventions. Local capacity will be further advanced through bespoke courses and ViGOR Research Fellowships. Finally, we will ensure the research is locally relevant and embedded within health systems infrastructure. Our project aligns closely with NIHR call 4 priorities in building resilience to the global threat from virus outbreaks, generating new leadership in LMICs, and undertaking high quality policy relevant research. It will serve as a template for what can be achieved in Africa, and the merits of investing in such reference laboratories throughout the continent. ViGOR has been developed in close consultation with the Partner institutes who work within their country’s Ministry of Health, enabling impact over the short, medium, and long term. Working with national reference laboratories will facilitate rapid dissemination of findings to public health authorities, and our established links to WHO AFRO and Africa CDC ensures findings feed into continent-wide planning.
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