Sierra Leone bolters mpox response: World Health Organization (WHO) leads groundbreaking genomic surveillance and bioinformatics training

In a strategic initiative aimed at enhancing mpox outbreak response and genomic surveillance capacity, the Central Public Health Reference Laboratory (CPHRL) in Freetown hosted the mpox Genomics and Bioinformatics training workshop  from 23rd – 27th June 2025. The event was organized under the theme: “Strengthening Genomic Surveillance Capacity for mpox Response in Sierra Leone,” with technical and financial support from the World Health Organization (WHO AFRO and WHO Sierra Leone).  The training program targeted 15 participants, including laboratory scientists, public health professionals, and epidemiologists from across Sierra Leone.

Despite reporting over 4,400 confirmed cases of mpox as of 27th 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 Ministry of Health and Sanitation (MoHS) and the Sierra Leone National Public Health Agency (SLNPHA) of Sierra Leone have prioritized strengthening genomic surveillance to enable rapid outbreak detection, track viral transmission, and inform policy decisions. Allan Campbell, Laboratory Lead at CPHRL, emphasized the significance of this training, stating, “This marks a pivotal moment in Sierra Leone’s national response to mpox. 

The initiative addresses the substantial bioinformatics capacity gap and establishes a foundation for sustainable genomic surveillance that can directly inform public health actions.” The workshop aligns with the objectives outlined in the WHO African Region (AFRO) Joint Continental mpox Response Plan 2.0, focusing on intensification, integration, and establishing a sustainable legacy in genomic epidemiology.

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.”

Doris Harding, Laboratory Pillar Lead at the SLNPHA, highlighted the broader implications: “Strengthening our capacity for genomic surveillance is no longer optional—it is essential. This initiative empowers our scientists to respond more effectively to mpox and other emerging pathogens.” Similarly, Jonathan Greene, WHO Sierra Leone Laboratory Lead, articulated the importance of workforce development, asserting, “Building a skilled, locally capable workforce is central to WHO’s strategy for resilient health systems. The use of genomics is transforming outbreak intelligence, enabling a shift from reactive to proactive responses.” 

Dr. Ameh George, WHO Representative in Sierra Leone, emphasized the strategic importance of institutionalizing genomic surveillance: “Genomics is redefining outbreak science. Sierra Leone must lead in generating and utilizing genomic data to inform policy and strengthen global health security. WHO remains committed to supporting this transformation.”

Participants and stakeholders concurred that this training initiative constitutes a long-term investment in Sierra Leone’s epidemic preparedness, response and resilience. By decentralizing sequencing capabilities and integrating genomic data into national decision-making processes, the program aspires to support regional efforts for early detection and rapid response to outbreaks.

The workshop concluded with the issuance of certificates of completion and a networking session aimed at fostering collaboration and innovation in public health genomics. As Sierra Leone advances its surveillance infrastructure, the overarching goal remains to elevate genomic data from an underutilized resource to a central element of outbreak response and epidemic intelligence, thereby strengthening national and regional health security.

Distributed by APO Group on behalf of World Health Organization – Sierra Leone.