The World Health Organization African region has the greatest infectious disease burden in the world. However, many African countries have limited capacity to rapidly detect, report, and respond to public health events. The Centre for Epidemic Response and Innovation (CERI), KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) in South Africa, and global Climate Amplified Diseases and Epidemics (CLIMADE) consortium are investing in building the capacity of African scientists in pathogen genomics and bioinformatics. A two-week long (11–21 April 2023) intensive training in wet-laboratory genomic data production, bioinformatics, and phylogenetic analyses of viral and bacterial pathogens was held in Cape Town, South Africa. Training was provided to 36 fellows with diverse backgrounds from 16 countries, 14 of which were low- and middle-income African countries. In this report, we, the fellows, share our collective experiences and describe how the learnt skills have been integrated into the operations of our home institutions to advance genomic surveillance capabilities. We identified the in-person and hands-on learning format of the training, taught by genomics experts and field application specialists, as the most impactful elements of this training event. Adaptation and miniaturisation of protocols to detect other pathogens is a great enhancement over the traditional method of using a single protocol for a pathogen. We note the duration of the training as the largest limiting factor, particularly for the computationally intensive bioinformatics sessions. We recommend this programme continue to build pathogen genomics capacity in Africa.

The global prevalence of resistance to antiviral drugs combined with antiretroviral therapy (cART) emphasizes the need for continuous monitoring to better understand the dynamics of drug-resistant mutations to guide treatment optimization and patient management as well as check the spread of resistant viral strains. We have recently integrated next-generation sequencing (NGS) into routine HIV drug resistance (HIVDR) monitoring, with key challenges in the bioinformatic analysis and interpretation of the complex data generated, while ensuring data security and privacy for patient information. To address these challenges, here we present HIV-DRIVES (HIV Drug Resistance Identification, Variant Evaluation, and Surveillance), an NGS-HIVDR bioinformatics pipeline that has been developed and validated using Illumina short reads, FASTA, and Sanger ab1.seq files.

Genomic technologies are transforming infectious disease surveillance and control, particularly in resource-limited settings such as Uganda. This review examines ongoing efforts by the Department of National Health Laboratory and Diagnostic Services - Central Public Health Laboratories (NHLDS-CPHL) to integrate genomics into public health strategies. We highlight key advancements, lessons learned, and opportunities, including expanded genomic testing capacity, localized bioinformatics infrastructure, and reinforcement of surveillance systems. Through use-case studies on COVID-19, HIV/AIDS, malaria, Ebola, Mpox, rotavirus, and cholera, we demonstrate the impact of genomics on improving diagnostic accuracy, disease monitoring and outbreak response, identifying drug resistance, and informing targeted public health interventions. Despite these successes, challenges, including but not limited to infrastructure gaps, funding constraints, and ethical considerations, remain, underscoring the need for policy, regulation, and capacity enhancement as well as global collaboration to effectively address these obstacles. Lessons learned from these efforts provide valuable recommendations for optimizing and sustaining genomic programs in low-resource settings. By leveraging genomics, Uganda can further strengthen its ability to detect, monitor, and respond to emerging and re-emerging health threats, ultimately enhancing disease control measures and public health resilience.