Evidence-led policymaking for COVID-19 control relies on accurate understanding the epidemiology of SARS-CoV-2 infections by correlating diagnostics, molecular fingerprinting and patient metadata (intrinsic (e.g. age), and extrinsic (e.g. travel history)). Efforts to correlate these data in Uganda are stalling, despite available local expertise, because laboratories designated for diagnosing and tracking COVID-19 are under-resourced, and widespread mistrust of diagnostic workflows. Current policy is therefore shaped by data from industrialised countries, which may be misleading due to significant differences in the population demographics and underlying health status. Laboratory facilities in northern Uganda are lacking: i) reagents and experience of reliable workflows for processing of COVID-19 diagnostics; ii) whole genome sequencing equipment and consumables for providing robust epidemiological information. We will address these needs by bringing together UK-based academics and industrial partners with Ugandan biologists and policymakers to rapidly build local capacity for SARS-CoV-2 diagnostics and real-time epidemiology. Specifically: Transfer knowledge of SARS-CoV-2 diagnostic workflows from leading UK testing centres (NHS, Lighthouse Labs) to Uganda. Establish Nanopore sequencing and bioinformatics in northern Uganda, supported by Salford/Liverpool/COG-UK partners, and facilitate their long-term adoption by Ugandan laboratories (UVRI, Makerere University). Combine WGS with new survey-based patient metadata to provide real-time SARS-CoV-2 genomics, including strains circulating around refugee settlements, to support the Ugandan Ministry of Health and Prime Minister's Office to promptly mitigate local and national COVID-19 spread. Bring together industry and logistics partners with Ugandan policymakers, to identify and address bottlenecks in the equipment and consumable supply chain, to support cost-effective, future Ugandan bioscience.