Inside the Institut Pasteur de Dakar’s field deployment, where sequencing, diagnostics and epidemiological modeling converged into Africa’s most sophisticated mpox response to date.
In a webinar hosted by Xpedite Diagnostics, scientists from the Institut Pasteur de Dakar (IPD) unpacked their real-time deployment to Sierra Leone, three months of intense field genomics, epidemiological troubleshooting, and data-driven decision support. Their findings reveal a new blueprint for outbreak response in low-resource settings: decentralized sequencing, community-level case detection, and predictive modeling operating in real time.
Introduction
When the first patients arrived at hospitals in Freetown with painful rashes in early January 2025, no one imagined that Sierra Leone would soon face one of West Africa’s largest recorded Mpox outbreaks. The early cases came quietly, young adults, mostly men, many with lesions they didn’t talk about until the pain forced them to seek care. By March, clinicians across the Western Area were reporting more patients with similar symptoms. Something was building.
The numbers kept rising. By the end of October, the country had counted over 6,000 suspected cases and more than 5,000 laboratory-confirmed infections, most of them concentrated in dense, hard-to-track neighborhoods around Freetown.
But inside that difficult year, something new was taking place, something many in Sierra Leone’s health system had never witnessed before. For the first time, genomic sequencing, rapid diagnostics, and field epidemiology were woven together in real time. Sierra Leonean laboratorians, epidemiologists, nurses, and community monitors were at the center of it, working side by side with colleagues from the Institut Pasteur de Dakar (IPD) response team including Dr. Martin Faye, Dr. Mamadou Aliou Barry and Dr. Gaye Aboubacry, to map an outbreak as it was developing.
The story of this outbreak is a story of science, collaboration and deeply local.
The First Genomes Arrive
Sierra’s public health infrastructure had grown dramatically since the dark days of Ebola. But Mpox was spreading fast, and national laboratories were stretched. The request was simple: help us see the virus clearly enough to act.
IPD received 18 clinical samples for sequencing. The genome sequencing data came back within three days.
They contained some interesting data.
Two sub-lineages of Clade IIb were circulating simultaneously, A.2.2 and B.1.6, closely related to viruses recently seen in neighboring Côte d’Ivoire. And when the team reconstructed the viral phylogeny, new insights emerged: the virus had likely entered the country months earlier, around late September 2024, moving quietly through networks that no one had thought to monitor.
This revelation didn’t cause panic. Instead, it sharpened the response. The outbreak wasn’t fast, it was quiet, steady, and slow-burning. That kind of outbreak requires different tools.
Sierra Leone now had the blueprint.
Building the Response: Local Hands, Local Knowledge
The most striking thing about the June deployment is that nothing about it felt like an external intervention. IPD brought equipment, sequencing platforms, and additional expertise, but Sierra Leonean laboratorians, epidemiologists, and data teams led the work on the ground.
At the Port Loko Governmental Hospital, technicians worked through long nights processing samples with persistence. Portable nanopore sequencers ran on backup power when the grid flickered. The first sequencing runs in-country produced clean, high-coverage genomes, a moment of genuine pride.
Mobile diagnostic labs were set up in Port Loko and Kabala, not because the team had a strategic blueprint, but because local health officers knew exactly where the bottlenecks were. They understood which districts were losing precious time because samples had to travel for hours before reaching a testing site. Their instinct proved right: local testing dramatically reduced delays and revealed hidden chains of transmission.
Both labs operated with Xpedite Diagnostics SwiftX™ extraction workflows, allowing rapid turnarounds even with inconsistent electricity and variable sample quality.
As Dr. Martin Faye noted:
“Science only works if it respects the people and the systems already here.”
And in Sierra Leone, that meant sitting with district health officers, adapting protocols to local conditions, and letting field realities shape the scientific approach, not the other way around.
A Turning Point: Changing the Case Definition
One of the breakout insights came not from a genome, but from patient observation.
Clinicians in Freetown and Port Loko began pointing out a pattern: almost every patient they admitted had genital lesions, many severe. These lesions weren’t listed in the national case definition. As a result, countless cases never reached health facilities, they were managed privately, quietly, and often too late.
Dr. Mamadou Aliou Barry worked with Sierra Leonean clinicians to correct this oversight. Together, they advocated for a new case definition that included genital lesions and expanded community-based active search.
The effect was immediate: more early-stage cases detected, fewer severe presentations, better referral pathways, more trust in the system.
What the Genomes Revealed
As sequencing scaled up, a clearer picture of the outbreak emerged.
More than 400 genomes were sequenced, an unprecedented volume for Sierra Leone. When these genomes were linked with case data, travel histories, and timelines, a pattern crystallized:
Western Area Urban was the outbreak’s “circulation engine.”
From here, the virus spreaded outward.
71 inter-district transmission events traced back to Western Area Urban. 52 inter-regional events followed the same path.
These weren’t artificial findings, they matched what community health workers had been saying all along: mobility in and out of Freetown was driving the outbreak more than anything else.
Another insight surprised many: there were no new introductions after the initial seeding. Everything after December was local transmission.
Genome by genome, the outbreak’s "story" became visible.
At the time of deployment, case investigation forms and laboratory data streams were fragmented. The IPD team deployed an integrated digital platform with:
- real-time dashboards;
- sample tracking;
- case-mapping (geo-referenced);
- automated epidemic curves;
- genomic-epidemiological data fusion.
Forcasting a Pandemic
In August, modelers at IPD and NPHA merged sequencing data with real-time case curves. Their projections suggested that by Week 38, the outbreak would begin to collapse.
By Week 42, the forecast had come true: only five confirmed cases remained.
For the first time in a Sierra Leonean outbreak, models weren’t post-mortems. They were tools for live decision-making. And they were being interpreted by Sierra Leonean epidemics officers who understood how each curve reflected events happening in their districts.
Vaccination campaigns were timed around these projections. Supplies were allocated based on forecasted district-level peaks. Districts preparing for possible surges were given early warning.
This is what outbreak intelligence looks like when it’s driven by partnership rather than pipeline.
A New Public Health Landscape in Africa
Today, the mobile labs remain active. The technicians who learned sequencing during the outbreak are now the trainers. Data systems that once lived in spreadsheets now run as real-time dashboards. And Sierra Leone has joined a growing West African genomic network, one built on open data, shared tools, and mutual trust.
The lingering challenges are real. Vaccination coverage remains low (<2.5%), and mistrust in health systems persists in pockets. But the infrastructure is no longer fragile. It’s growing roots.
In the words of one Sierra Leonean laboratorian:
“We didn’t just respond to an outbreak. We built something that will outlive it.”
The Takeaway: Outbreak Response Works When It Belongs to the People Living Through It
The Sierra Leone mpox outbreak wasn’t defined by the number of cases. It was defined by what the country did with information, how data became insight, insight became action, and action became a path forward.
This is not a story of rescue. It is a story of shared expertise, local leadership, and science grounded in community realities.
It is also a reminder that genomic surveillance becomes powerful not when it is advanced, but when it is trusted, shared, and used by the people closest to the outbreak.
And that is exactly what happened here.
Bring high-performance extraction to real-time outbreak surveillance
SwiftX™ workflows are engineered for field deployments, mobile labs, and decentralized sequencing, delivering consistent DNA recovery even with variable sample quality, limited power, or challenging logistics.
Use the same extraction technology that supported the Institut Pasteur de Dakar Mpox response in Sierra Leone.
- Contact us to integrate SwiftX toolbox into your surveillance, sequencing, or diagnostic workflows.
- Watch again the full webinar for the complete field deployment analysis.