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Early epidemiologic and genomic insights from Sierra Leone's first mpox cases, 2025.

Eric Nzirakaindi Ikoona·Gebrekrstos Negash Gebru·Martin Faye·Bridget Magoba·Doris Harding·Mary Magdalene Sinnah·Mustapha Jalloh·Fatou Diène Thiaw·Aminata Tigiedankay Koroma·Serigne Fallou Mbacké Ngom·Joseph Sam Kanu·James Sylvester Squire·Landry Gerald Boussiengui·Ndongo Dia·Ousmane Faye·Boubacar Diallo·Abdourahmane Sow·Mohamed Alex Vandi·Sartie Kenneh·Austin Demby·Foday Sahr
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Abstract

INTRODUCTION: early characterization of outbreak cases supports rapid decisions. We conducted real-time analysis during the initial outbreak phase in mid-March 2025 of Sierra Leone's first 44 laboratory-confirmed Mpox cases (10th January to 5th March 2025) to generate epidemiologic and genomic intelligence for response. METHODS: we summarized surveillance data and sequenced 18 early cases with Oxford Nanopore. Firth-penalized logistic regression was employed to explore risk factors for severe disease. RESULTS: median age was 27 years (interquartile range 22 to 35); 68.2% were male. Most cases reported no recent international travel (95.5%). All cases presented with rash; fever occurred in 72.7%. Six cases (13.6%) met severe criteria; no deaths occurred (0 of 44; 95% confidence interval 0 to 8.0). Household secondary attack rate was 7.3% during the study window and 8.2% after completion of follow-up. Sequencing identified two co-circulating sub-lineages consistent with A.2.2 and B.1.6 and a strong APOBEC3 pattern (142 of 212 guanine-to-adenine in thymine-cytosine versus 70 of 212 cytosine-to-thymine in guanine-adenine; exact binomial p approximately 8.6x10-7; X2= 24.5, df = 1, p≈ 7.6x10-7). Root-to-tip analysis showed weak temporal signal (R2=0.31; date randomization p= 0.18), so we did not interpret clock estimates. CONCLUSION: real-time analysis during the initial outbreak phase showed community transmission, quantified household spread, documented two sub-lineages with an APOBEC3 signature, and generated severity hypotheses that immediately informed surveillance and vaccine prioritization. Findings require validation in larger cohorts.

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AdultFemaleHumansMaleYoung AdultDisease OutbreaksFeverGenomicsLogistic ModelsRisk FactorsSierra LeoneMpox, MonkeypoxMonkeypox virusMpoxWest Africaepidemiologygenomic surveillanceoutbreak investigationrapid responseJournal Article

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Eric Nzirakaindi Ikoona, Gebrekrstos Negash Gebru, Martin Faye, Bridget Magoba, Doris Harding, Mary Magdalene Sinnah, Mustapha Jalloh, Fatou Diène Thiaw, Aminata Tigiedankay Koroma, Serigne Fallou Mbacké Ngom, Joseph Sam Kanu, James Sylvester Squire, Landry Gerald Boussiengui, Ndongo Dia, Ousmane Faye, Boubacar Diallo, Abdourahmane Sow, Mohamed Alex Vandi, Sartie Kenneh, Austin Demby, Foday Sahr. 2026-04-29. Early epidemiologic and genomic insights from Sierra Leone's first mpox cases, 2025.. https://doi.org/10.11604/pamj.2026.53.177.49795

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