Epidemiology and phylogenomic characterisation of two distinct mpox outbreaks in Kinshasa, DR Congo, involving a new subclade Ia lineage: a retrospective, observational study.

Abstract

Background Clade I monkeypox virus is endemic in DR Congo. We aim to describe the epidemiological trends of the cocirculating subclades Ia and Ib mpox outbreaks in Kinshasa, DR Congo.Methods This retrospective observational study included suspected and laboratory-confirmed mpox cases reported between Jan 1, 2023, and Oct 31, 2024, in Kinshasa. Skin lesion swabs or blood samples were collected as part of a routine countrywide mpox surveillance programme. To confirm the diagnosis of mpox, all samples were tested at the Institut National de Recherche Biomédicale (INRB) using real-time PCR. Whole-genome sequencing was conducted for phylogenomic analysis and assessment of APOBEC3 type mutations. Samples that remained unassigned to subclade Ia or Ib after whole-genome sequencing and real-time PCR were labelled as an unknown subclade.Findings As part of routine disease surveillance, 1479 suspected mpox cases were reported in Kinshasa. Samples were collected from 1314 suspected mpox cases and tested by PCR at the INRB. 440 (34%) of 1314 suspected cases had PCR confirmed mpox, with the first confirmed mpox case detected on Aug 18, 2023. 262 (60%) of 440 cases were male, 172 (39%) were female, and six (1%) were unknown, and the median age was 26 years (IQR 19-34). The epidemiological curve suggests two distinct periods during the 2023-24 outbreaks in Kinshasa. Between Aug 18, 2023, and June 30, 2024 (period 1), 218 suspected mpox cases underwent investigation and 24 (11%) were PCR confirmed as mpox; all cases were identified as subclade Ia. After a decline in suspected and confirmed cases in early 2024, the first confirmed subclade Ib mpox case in Kinshasa was reported on July 1, 2024. Between July 1 and Oct 31, 2024 (period 2), 1096 suspected mpox cases were reported and 416 (38%) were PCR confirmed as mpox. In-depth epidemiological case investigations during period 1 identified three small, self-limiting transmission chains between August and September, 2023. Case investigation data were available for 127 cases with PCR confirmed mpox, including clinical symptom data available for 61 (64%) of 95 with subclade Ia. The most commonly reported symptoms were fever (49 [80%] of 61) and skin rash (48 [79%]). The most common lesion locations were genital or anorectal (35 [64%] of 55 cases with available data). Case investigation data were available for 32 cases with subclade Ib mpox, including clinical symptom data available for 21 (66%) with subclade Ib. The most commonly reported symptoms were skin rash (18 [86%] of 21) and fever (12 [57%]). Genital or anorectal involvement was reported in 13 (68%) of 19 cases with available lesion location data. Genomic analysis shows five separate self-limiting clusters of subclade Ia (group II sampled from August, 2023, to August, 2024) and two larger clusters (occurring from July, 2024, to October, 2024, in period 2) belonging to subclade Ia (group II) and subclade Ib. 32 (68%) of 47 mutations for subclade Ia cluster outbreak and 28 (72%) of 39 mutations for subclade Ib outbreak were consistent with APOBEC3 driven changes.Interpretation Sustained human-to-human transmission occurred after repeated self-limiting introductions of subclade Ia documented since 2023, which has cocirculated with subclade Ib in Kinshasa from July, 2024. Increased APOBEC3 driven changes in the new subclade Ia lineage support a shift towards human-to-human transmission. These findings reveal important changes in mpox transmission dynamics and suggests that any monkeypox virus subclade has the potential to cause sustained human outbreaks when favourable transmission conditions are met.Funding Belgian Directorate-General for Development Cooperation and Humanitarian Aid; the Research Foundation Flanders; Institute of Tropical Medicine Structurele Onderzoeksfinanciering (Flemish Government; Science, Technology, and Innovation); Global Health European and Developing Countries Clinical Trials Partnership 3 Joint Undertaking; the US Department of Defense Threat Reduction Agency; the US Department for Agriculture Research Service; Canadian Institutes of Health Research; International Development Research Centre; US National Institute of Allergy and Infectious Diseases, National Institutes of Health; and Wellcome Trust.