Genomic
Surveillance
Genomics Research Delivering high-throughput sequencing and pathogen surveillance to detect, track, and understand infectious diseases across Africa — providing real-time genomic intelligence that informs outbreak response, vaccine evaluation, and epidemic forecasting.
What the Team
Investigates
Sequencing viruses, bacteria, and other pathogens at scale using Illumina, Oxford Nanopore, and Sanger platforms for rapid genomic characterisation.
Real-time genomic surveillance of emerging variants, outbreak clusters, and novel pathogens across Africa to support early detection and response.
Identifying and characterising zoonotic pathogens at the human-animal interface with genomic tools to support early warning and containment.
Investigating resistance at the human-animal-environment interface to understand cross-species transmission and environmental reservoirs.
Providing genomic data to support vaccine efficacy assessments, escape mutation monitoring, and evaluation of immune responses at population scale.
Integrating genomic intelligence with epidemiological models to forecast outbreak trajectories and inform public health decision-making.
From Sample
to Surveillance
Clinical, animal, and environmental samples received from health facilities, surveillance networks, and partner organisations across Africa.
Nucleic acid extraction, library preparation, and quality control to ensure high-quality sequencing inputs for downstream analysis.
High-throughput sequencing on Illumina NovaSeq, NextSeq, Oxford Nanopore GridIon, and Sanger platforms for short and long-read data.
Assembly, annotation, variant calling, and phylogenetic analysis using validated pipelines developed by the Bioinformatics Unit.
Genomic data shared to GISAID, GenBank, and national health authorities with real-time surveillance reports and policy briefs.
Pathogens Under
Genomic Surveillance
Research &
Partner Network
Building and maintaining the genomic analysis pipelines that process all sequencing output at scale.
Running the sequencing platforms including Illumina NovaSeq, NextSeq, and Oxford Nanopore GridIon.
Contributing genomic data to continental surveillance platforms and supporting pandemic preparedness across Africa.
Providing real-time genomic intelligence to national public health authorities to inform outbreak response decisions.
Meet the
Team
Latest
Publications
International Journal of Infectious Diseases 162:108162
Clinical Microbiology and Infection 32:192-195
Nature Methods 23:653-662
Nature Ecology & Evolution 10:610-610
Emerging Microbes & Infections
Nature Communications 28;16(1):4937. doi: 10.1038/s41467-025-60081-0
BMJ Global Health 10(6):e018297. doi: 10.1136/bmjgh-2024-018297.