The Mpox outbreak in Sierra Leone has challenged national health systems and tested the speed of real-time genomic response across West Africa. In this webinar, hosted by Xpedite Diagnostics, scientists from the Institut Pasteur de Dakar (IPD) shared first-hand insights from the field, detailing how genomic sequencing, RT-PCR diagnostics, and data-driven epidemiology supported outbreak containment and informed global health preparedness.
Emerging infectious diseases thrive in the seams of surveillance where ecology, mobility, and data gaps converge. Between January and October 2025, Sierra Leone reported more than 6,000 suspected Mpox cases and over 5,000 confirmed infections, concentrated around Freetown’s densely populated western districts. The Institut Pasteur de Dakar, in collaboration with Sierra Leone’s National Public Health Agency (NPHA), deployed multidisciplinary teams integrating molecular diagnostics, bioinformatics, and epidemiological modeling to support national response coordination.
Tracking the Outbreak: From First Detection to Genomic Mapping
Dr. Martin Faye, a virologist at IPD specializing in orthopoxvirus genomics, presented an overview of the outbreak’s evolution and the rapid sequencing efforts that defined its early phase. The first confirmed cases emerged in January 2025, with IPD receiving 18 clinical samples for next-generation sequencing. Within three days, the team generated complete viral genomes, confirming the circulation of two clade IIb sublineages A.2.2 and B.1.6, closely related to strains previously detected in Côte d’Ivoire.
These findings enabled the identification of transmission hotspots in Freetown’s West Area Urban and West Area Rural districts, prompting the declaration of a national public health emergency by late May.
IPD’s field teams deployed mobile laboratories in Port Loko and Kabala, conducting RT-qPCR and rapid isothermal amplification testing on-site, supported by SwiftX™ DNA extraction workflows. Genomic data integration and real-time dashboards enabled decision-makers to visualize case trends and guide vaccination campaigns across affected regions.
Integrating Diagnostics, Data Science, and Field Epidemiology
Dr. Mamadou Aliou Barry, infectious disease epidemiologist and outbreak preparedness expert, expanded on coordination and case management strategies. He described how the team participated in daily incident management meetings with WHO, Africa CDC, and local partners to optimize data collection and community engagement.
Barry’s team identified a crucial surveillance gap: early case definitions failed to include genital lesions, a dominant clinical sign observed in nearly all hospitalized patients. Updating this definition, alongside community-based active case search, helped shift surveillance from hospital-based detection to early community containment.
He also detailed improvements in case referral, pharmacy outreach to discourage self-medication, and the establishment of mortality audits to investigate fatal cases and refine clinical management protocols.
Data Integration and Predictive Modeling for Outbreak Control
Dr. Aboubacry Gaye, data scientist at IPD, highlighted how genomic and epidemiological datasets were merged into a real-time analytics dashboard, supporting risk-based decision-making. The modeling framework projected that, by week 38 of 2025, the number of active cases would decline to near zero, a forecast later confirmed by surveillance data showing only five new cases by week 42.
By integrating sequencing data from over 300 whole genomes, IPD identified 71 inter-district and 52 inter-regional transmission events, confirming the Western Area Urban district as the primary dissemination hub. Genomic analysis also revealed that the virus likely entered Sierra Leone three months before detection, around September 2024, highlighting the critical value of proactive molecular surveillance.
Capacity Building and Regional Preparedness
Beyond outbreak control, the IPD team emphasized sustainable capacity building. Mobile labs established in Sierra Leone remain operational, with local technicians now independently conducting Mpox diagnostics and sequencing. The collaborative model, combining rapid genomic response, open data sharing, and cross-border laboratory networks, offers a scalable blueprint for regional epidemic preparedness.
As Dr. Faye noted, “We cannot predict where the next outbreak will emerge, but we can be ready.” The team’s collaboration with Sierra Leone’s NPHA, ECOWAS, and partners from the PREPARE-TID consortium exemplifies how decentralized genomic infrastructure can transform Africa’s outbreak response capabilities.
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