Infectious Diseases
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Pathogen genomics, epidemiology and surveillance analysis for the infections that carry Africa's heaviest burden.
Infectious disease research is where our consultants have done most of their work, and where analysis capacity in Africa is most visibly stretched. Sequencing platforms installed during the COVID-19 response are now producing data on tuberculosis, malaria, cholera, HIV, arboviruses and antimicrobial resistance — often faster than it can be interpreted.
We support that work as an analysis partner: per-project for individual studies, or as a standing arrangement for surveillance programmes that need results on a fixed weekly or monthly cycle.
Pathogens and Programmes We Support
The same underlying analysis capability, tuned to the organism.
Respiratory Viruses
SARS-CoV-2, influenza and RSV: consensus assembly from amplicon or shotgun data, lineage and clade assignment, variant tracking over time, and submission-ready packages for GISAID, ENA and NCBI.
Mycobacterium tuberculosis
Whole genome analysis for lineage assignment, drug resistance prediction against WHO-catalogued mutations, mixed infection detection and transmission cluster reconstruction.
Plasmodium falciparum
Drug resistance marker profiling, pfhrp2/3 deletion detection affecting rapid diagnostic test performance, complexity of infection estimation and parasite population genomics.
Bacterial Pathogens and AMR
Cholera, typhoid, meningococcus and enteric pathogens: cgMLST typing, outbreak reconstruction, plasmid and mobile element analysis, and resistance profiling against CARD, ResFinder and AMRFinderPlus.
HIV and Viral Hepatitis
Subtyping, drug resistance mutation profiling against Stanford HIVdb, and phylogenetic analysis of transmission networks.
Arboviruses and Emerging Threats
Dengue, chikungunya, yellow fever, Lassa, Rift Valley fever and Mpox: assembly from low-titre samples, lineage assignment and phylogeographic reconstruction of introductions.
Beyond Genomics
Epidemiological and surveillance analysis
Sequence data alone rarely answers a public health question. We pair it with the epidemiological analysis that gives it meaning:
- Epidemic curves, effective reproduction number estimation and outbreak projections
- Vaccine effectiveness and coverage analysis from routine and trial data
- Spatial and spatio-temporal analysis of case distribution and hotspot detection
- Time-series analysis of routine surveillance and health information system data
- Diagnostic test evaluation with appropriate confidence intervals
- Antimicrobial resistance trend analysis across sentinel sites
Working with surveillance programmes
Surveillance is a rhythm, not a project. Programmes we support on a standing basis get an agreed turnaround per batch, a standardised report format suitable for circulation to health authorities, and training so laboratory staff progressively take the pipeline in-house.
We would rather work ourselves out of a surveillance contract by building your team's capacity than hold the analysis indefinitely.
Why local analysis matters scientifically
Reference databases and lineage nomenclature systems are built disproportionately on sequences from Europe, North America and Asia. Novel African lineages are frequently assigned poorly or flagged as low quality by tools that have not seen them before. Analysts who work with African pathogen data routinely recognise that pattern instead of discarding the sequence.
