Sierra Leone Strengthens Genomic Surveillance to Combat Rising Mpox Cases

In a landmark effort to reinforce epidemic preparedness and public health resilience, the Central Public Health Reference Laboratory (CPHRL) in Freetown hosted a comprehensive Mpox Genomics and Bioinformatics Training Workshop from June 23 to 27, 2025. With technical and financial backing from the World Health Organization’s African Regional Office (WHO AFRO) and WHO Sierra Leone, the event was themed “Strengthening Genomic Surveillance Capacity for Mpox Response in Sierra Leone.”

This initiative is particularly timely, as Sierra Leone has reported over 4,400 confirmed mpox cases as of June 27, 2025. Yet, only about 2.5% of these cases (108 genomes) have been sequenced and characterized, highlighting a critical gap between outbreak detection and genomic data generation—a shortcoming that hampers real-time surveillance, variant tracking, and effective public health interventions.

Elevating Genomics from Data to Action

The training workshop brought together 15 participants—a mix of laboratory scientists, public health professionals, and epidemiologists from various regions of Sierra Leone. Its objective: to build national capacity for genomic surveillance, enabling the country to track viral evolution, detect emerging variants, and apply data-driven strategies in managing outbreaks.

“This marks a pivotal moment in Sierra Leone’s national response to mpox,” said Allan Campbell, Laboratory Lead at CPHRL. “The initiative addresses the substantial bioinformatics capacity gap and establishes a foundation for sustainable genomic surveillance that can directly inform public health actions.”

The program aligns with WHO AFRO’s Joint Continental mpox Response Plan 2.0, which prioritizes intensifying surveillance, integrating genomic epidemiology into national strategies, and institutionalizing sustainable capacity building across the continent.

A Deep Dive into Hands-On Training

The five-day workshop employed a practical, multidisciplinary approach—blending theoretical instruction with real-time data analysis. Participants worked through a carefully structured curriculum:

• Day 1: Introductions to genomic surveillance principles, sequencing technologies, and foundational tools like Linux, Conda, and command-line environments.

• Day 2: Sequencing data quality control using FastQC, MultiQC, and read preprocessing tools like Fastp and Hostile. Genome assembly techniques via BWA, Cutadapt, and SPAdes were introduced.

• Day 3: Participants explored variant detection with SAMtools, FreeBayes, and Snippy. Tools like Bcftools, SnpEff, and VEP were used for consensus sequence generation and genome annotation.

• Day 4: Phylogenetic analysis and clade classification using Nextclade, Nextstrain, and data visualization via Microreact, GISAID, Pathoplexus, NCBI Virus, iTOL, and Galaxy.

• Day 5: A full simulation of an mpox outbreak response involving strategic data interpretation, cross-functional collaboration, and drafting of genomic-informed public health recommendations.

Building Bioinformatics Capacity for the Future

Leading the training was Walter Oguta, WHO AFRO’s EPI Analytics Specialist, who emphasized the workshop’s emphasis on practical utility.

“Translating genomic data into actionable public health strategies is the ultimate goal,” Oguta said. “Our aim was to equip participants with both technical proficiency and the confidence to apply these tools in real-world outbreak scenarios.”

Doris Harding, Laboratory Pillar Lead at the Sierra Leone National Public Health Agency (SLNPHA), highlighted the strategic 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.”

Toward a Resilient Health System

Jonathan Greene, WHO Sierra Leone Laboratory Lead, echoed this sentiment, stressing the centrality of local workforce development:

“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.”

The importance of institutionalizing genomic capabilities was further reinforced by Dr. Ameh George, WHO Representative in Sierra Leone:

“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.”

Integrating Genomics into National Policy

The workshop comes amid growing momentum within the Ministry of Health and Sanitation (MoHS) and the SLNPHA to embed genomic tools into national health policy. With global repositories such as GISAID, Pathoplexus, and NCBI Virus already hosting Sierra Leonean genomic data, the goal now is to decentralize sequencing, enhance real-time analysis, and integrate findings into decision-making structures.

Participants agreed that the training constitutes a long-term investment in national health security. By reducing dependence on external sequencing centers and empowering local scientists, the country is positioning itself to lead regional efforts in early detection, rapid response, and genomic epidemiology.

Closing and Future Collaborations

The workshop concluded with a certification ceremony and networking session, paving the way for a national genomic surveillance community of practice. Discussions included potential partnerships with universities, international agencies, and private labs to ensure sustained knowledge transfer and innovation.

Looking ahead, Sierra Leone’s commitment to genomic integration aims not only to improve mpox response, but also to build a health system agile enough to confront future pandemics, antimicrobial resistance, and emerging zoonotic threats.

As Africa continues its digital and scientific leap in public health, Sierra Leone’s proactive steps in genomics and bioinformatics are a beacon for resilient, data-driven health governance across the region.