Public Health

Despite reporting over 4,400 confirmed cases of mpox as of 27 June 2025, Sierra Leone has performed genomic characterization on only approximately 2.5% of these cases (108 sequences), representing a significant limitation in understanding viral evolution and informing targeted public health interventions. Currently, these genomic data are deposited in international repositories such as Pathoplexus, GISAID, and NCBI Virus; however, the disparity between outbreak detection and genomic data generation hampers real-time surveillance efforts.

The week-long workshop employed a multidisciplinary, hands-on approach combining didactic instruction, practical exercises, and group data analysis. The curriculum included:

• Day 1: Introduction to genomic surveillance principles, sequencing technologies, and foundational bioinformatics tools such as Linux and Conda environments.
• Day 2: Emphasis on sequencing data quality control (FastQC, MultiQC), read trimming (Fastp, Hostile), and genome assembly techniques utilizing reference-based (BWA, Cutadapt) and de novo (SPAdes) approaches.
• Day 3: Variant detection and analysis (SAMtools, FreeBayes, Snippy), consensus sequence generation (Bcftools), and genome annotation (SnpEff, VEP).
• Day 4: Phylogenetic analysis, clade classification (Nextclade, Nextstrain), and visualization using platforms such as GISAID, Pathoplexus, NCBI Virus, Microreact, iTOL, and Galaxy.
• Day 5: Integration of all components through a case study simulating mpox outbreak response, culminating in data interpretation and strategic planning.

Walter Oguta, WHO AFRO EPI Analytics Specialist and the Lead Bioinformatics Trainer, underscored the practical value of the training, stating, “Translating genomic data into actionable public health strategies is the ultimate goal. Our aim was to equip participants with both technical proficiency and confidence to utilize these tools effectively.”