🔬 Laboratory Science
Molecular diagnostics, genomic surveillance, and experimental platforms powering our infectious disease research in Burundi and the Great Lakes Region.
Our Laboratory Capacity
Our laboratory program bridges clinical observation with molecular epidemiology. Working with the National Institute of Public Health (INSP) and international partners, we apply cutting-edge diagnostic and genomic tools to characterise pathogen diversity, resistance, and transmission dynamics across Burundi.
Core Diagnostic Techniques
From rapid tests in the field to high-resolution genomic analysis
ELISA
Enzyme-Linked Immunosorbent Assay for quantitative detection of antibodies and antigens. Used for prevalence estimation and immunological profiling in population-level studies.
PCR & qPCR
Conventional and quantitative polymerase chain reaction for sensitive detection of pathogen DNA/RNA, enabling diagnosis of subclinical and asymptomatic infections.
RDT (Rapid Diagnostic Tests)
Highly sensitive and conventional RDTs for field-deployable diagnosis. We evaluate hrp2/3 deletion status causing false-negative results — critical for malaria control in Burundi.
Whole Genome Sequencing
End-to-end genomic sequencing of pathogens to characterise strain diversity, detect antimicrobial resistance mutations, and track outbreak origins and spread.
Phylogenetic Analysis
Reconstruction of evolutionary and transmission histories using molecular clock models. Enables inference of when and where outbreaks originated and how they spread.
Drug Resistance Genotyping
Molecular genotyping of resistance markers to antimalarials, antibiotics, and antivirals. Identifies resistance mutations early to inform treatment guidelines and control measures.
Genomic Data Analysis
Bioinformatics pipelines using Linux command-line tools and R for sequence alignment, variant calling, phylogenetic inference, and QGIS-based geographic mapping of genomic data.
Epidemiological Mapping
Spatial analysis of disease burden using QGIS and geostatistical methods. Generates risk maps to guide targeted interventions and health resource allocation.
Sequencing Platforms
Multi-platform capability for flexibility in pathogen genomics
Illumina
Short-read, high-accuracy whole genome sequencing for SNP detection and variant calling
Oxford Nanopore
Long-read, real-time sequencing enabling rapid outbreak response and structural variant detection
DNBSeq
High-throughput sequencing for population-scale genomic surveillance studies
CycloneSeq
Complementary platform for flexible pathogen sequencing in resource-limited settings
Pathogen Surveillance Portfolio
Active molecular and genomic surveillance of key infectious diseases
| Pathogen | Disease | Key Methods | Priority |
|---|---|---|---|
| Plasmodium falciparum | Malaria | qPCR, RDT, WGS, hrp2/3 genotyping, AMR markers | High |
| SARS-CoV-2 | COVID-19 | PCR, ELISA, WGS, Phylogenetics | High |
| Monkeypox virus | Mpox | PCR, WGS, AI-powered surveillance | High |
| Mycobacterium tuberculosis | Tuberculosis | PCR, AMR genotyping, WGS | Moderate |
| HIV-1 | HIV/AIDS | Phylodynamics, ELISA, RNA evolutionary models | Moderate |
| Vibrio cholerae | Cholera | PCR, WGS, AMR surveillance | Active |
| Zoonotic pathogens | Zoonoses | Molecular typing, risk mapping, QGIS | Ongoing |
Sample-to-Insight Workflow
From field collection to publication-ready findings
Field Collection
Clinical & community sampling
Lab Processing
Extraction & QC
Diagnostics
PCR, ELISA, RDT
Sequencing
Multi-platform WGS
Bioinformatics
Analysis & phylogenetics
Insights
Maps, models, policy
Laboratory Research Focus Areas
Key scientific questions our laboratory program addresses
- Asymptomatic malaria reservoir and transmission potential
- hrp2/hrp3 deletions causing false-negative RDTs
- Antimicrobial resistance genotyping in P. falciparum
- Pathogen evolutionary dynamics via phylogenetics
- Genomic surveillance of Mpox and SARS-CoV-2
- Performance evaluation of diagnostic tests
- HIV-1 genetic diversity in East Africa
- Zoonotic spillover risk characterisation
- RDT validation under field conditions
- AMR surveillance: cholera and TB