Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern—particularly Alpha, Beta, Delta, and Omicron—on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Mpox is a re-emerging zoonotic disease caused by MPXV, which has led to outbreaks across multiple countries in recent years. Sierra Leone reported its first mpox case in 8 years in January 2025, rapidly becoming the epicenter of a continental outbreak with more than 5,000 confirmed cases by August, a surge with unknown origins, timings and drivers. Phylodynamic analyses using 338 genomes generated from 14 districts suggests that the outbreak was caused by lineage G.1 (A.2.2.1) which descended from lineages circulating in Nigeria. Here we observed a strong APOBEC3 mutational enrichment, consistent with sustained human transmission that circulated undetected for ~3 months before the first confirmed case in January 2025. The Western Area Urban district served as the primary hub for nationwide spread and persistence, as well as multiple international export events. We further estimated that the true epidemic size was nearly double official case counts, highlighting substantial surveillance gaps. These findings underscore the urgent need for strengthened genomic and diagnostic surveillance systems across West Africa to pre-empt epidemics.

Background: Ebola virus emerged in West Africa in December 2013. The ease of mobility, porous borders, and lack of public health infrastructure led to the largest Ebola virus disease (EVD) outbreak to date. Intervention: The 2013 EVD outbreak signalled the need for laboratory diagnostic capabilities in areas without strong public health systems. As part of the United States’ Department of Defense response, MRIGlobal was contracted to design, fabricate, equip, deploy, and operate two mobile diagnostic laboratories (MDLs). The first laboratory analysed blood samples from patients in an adjacent Ebola Treatment Centre (ETC) and buccal swabs from the deceased in the community in Moyamba, Sierra Leone. The second laboratory was deployed to support an ETC in Conakry, Guinea. The Department of Defense provided real-time quantitative reverse transcription polymerase chain reaction assays that were deployed and validated on-site. Lessons Learnt: Prompt and accurate molecular diagnostics reduced sample turn-around times from over 24 h to under 4 h. Experienced laboratory staff tested up to 110 samples per day and on-site engineering proved necessary for MDL setup and operation. As the Ebola response slowed, the sustainment of the MDLs’ operations was prioritised, including staff training and the transition of the MDLs to local governments. Training programmes for local staff were prepared in Sierra Leone and Guinea. Recommendations: The MRIGlobal MDL team significantly contributed to establishing increased laboratory capacity during the EVD outbreak in West Africa. Using the MDLs for molecular diagnosis is highly recommended until more sustainable solutions can be provided.

In January 2025, Sierra Leone reported its first mpox case in eight years, followed by a rapid nationwide surge that made it the epicenter of the continental mpox virus (MPXV) Clade IIb A.2.2 outbreak, with more than 5,000 confirmed cases reported by August. To investigate the origin, timing, and spread of this epidemic, we generated 338 high-quality MPXV genomes from cases across 14 districts and conducted Bayesian phylogeographic analyses. We found that transmission was driven by a newly emerging Clade IIb lineage, G.1, descended from lineages circulating in the ongoing Nigerian epidemic. Phylogeographic reconstructions indicate that G.1 arose in late September 2024 and circulated undetected for approximately three months before establishing sustained transmission in the densely populated Western Area Urban and Rural districts, which became the principal source of repeated viral introductions that drove epidemics in other regions. Together, these findings reveal the origins and dispersal dynamics of the 2025 mpox outbreak in Sierra Leone and underscore that effective control remains achievable through targeted vaccination, strengthened early warning systems, and improved access to genomic and diagnostic surveillance.

Dengue is the leading mosquito-borne viral cause of human illness and death. More than four billion people globally live at risk of Dengue Virus (DENV) infection and most infections are asymptomatic or present with a non-specific febrile illness. In this report the first laboratory-confirmed dengue in Sierra Leone was identified one month after the launch of the national Syndromic Sentinel Surveillance Strategy (4S). A febrile adult tested RT-PCR–positive; we generated a near-complete genome assigned to DENV-2 genotype II, lineage F.1.1. Phylogenetically, the Sierra Leone genome formed a well-supported sister lineage with a 2024 USA genome, both nested within, but clearly diverged from, Indian sequences (2021–2022) and distinct from the Réunion clade. The degree of divergence is incompatible with a recent or direct import from South Asia lineages. It is more consistent with diversification in an undersampled Indian-Ocean/South Asia network or via unsampled intermediates outside Asia. No canonical NS4B resistance substitutions were detected. With a single Sierra Leone genome, the source and extent of local transmission remain unresolved. These findings underscore the benefits of integrating differential diagnostics and genomics into routine febrile-illness care and sustaining regional arboviral surveillance.

Dengue is the leading mosquito-borne viral cause of human illness and death. More than four billion people globally are at risk of dengue virus (DENV) infection, and most infections are asymptomatic or present with a non-specific febrile illness. We characterise the first complete DENV-2 genome from Sierra Leone, recovered from a febrile adult who tested RT-PCR–positive. The sequence was identified as DENV-2 genotype II, lineage F.1.1. Phylogenetically, the Sierra Leone genome formed a well-supported sister lineage with a 2024 USA DENV-2 genome; both were nested within but clearly diverged from Indian DENV-2 sequences (2021–2022) and were distinct from the Réunion DENV-2 clade. The degree of genetic divergence was incompatible with a recent or direct import of a South Asian lineage and was more consistent with diversification in an under-sampled Indian Ocean/South Asia network or outside this region in Africa. With a single Sierra Leone genome, the source and extent of local transmission remain unresolved. These findings underscore the benefits of integrating differential diagnostics and genomics into routine care for febrile illness and sustaining regional arboviral surveillance.