Epidemiology and Phylogenomic Characterization of Distinct 2023 and 2024 Mpox outbreaks in Kinshasa, Democratic Republic of the Congo - Evidence for increasingly sustained human-to-human transmission of subclade Ia
Authors: Wawina-Bokalanga Tony , Merritt Sydney , Kinganda-Lusamaki Eddy , Jansen Daan , Halbrook Megan , Pukuta-Simbu Elisabeth , O’Toole Áine , Hasivirwe Vakaniaki Emmanuel , Ola-Mpumbe Rilia , Kwete-Mbokama Papy , Akil-Bandali Prince , Kacita Cris , Ponga-Museme Ange , Mapenzi-Kashali Nelson , Amuri-Aziza Adrienne , Tshiani-Mbaya Olivier , Paku-Tshambu Princesse , Dantas Pedro HLF , de Block Tessa , Lokilo Emmanuel , Muswamba Chloé , Makangara-Cigolo Jean-Claude , Luakanda Gradi , Ngandu Christian , Kelvin David J. , Pratt Catherine , Ayouba Ahidjo , Tessema Sofonias , Ndembi Nicaise , Rezende Antonio Mauro , Delaporte Eric , Mwamba Dieudonné , Subissi Lorenzo , Liesenborghs Laurens , Hoff Nicole A. , Peeters Martine , Low Nicola , Ahuka-Mundeke Steve , Muyembe-Tamfum Jean-Jacques , Rimoin Anne W. , Kindrachuk Jason , Vercauteren Koen , Rambaut Andrew , Mbala-Kingebeni Placide 
Published: November 2024

ABSTRACTBackgroundMonkeypox virus (MPXV) is endemic to the Democratic Republic of the Congo (DRC), and historically has been reported in rural, forested regions with limited household and primarily zoonotic transmission. With the emergence of subclade Ib and increasing reported human-to-human transmission of MPXV we sought to characterize both the epidemiologic and genomic characteristics of confirmed mpox cases in Kinshasa, DRC, following confirmed MPXV introduction in August 2023.MethodsThis retrospective observational study leveraged demographic and case-investigation data, as well as biological samples, collected from suspected mpox cases in Kinshasa from January 2023 to September 2024 as part of routine national surveillance. Samples were tested at the Institut National de Recherche Biomédicale first by qPCR to confirm MPXV, and subsequently sequenced for genomic analysis for those samples with a cycle threshold value <31.FindingsEpidemiological characterization of all confirmed mpox cases in Kinshasa indicated two distinct periods of MPXV introduction and circulation: first, following the initial case in August 2023, self-limiting transmission chains of subclade Ia primarily among men. Case investigations from this period suggest human-human transmission. The second period is marked by the introduction of subclade Ib to the city and expanded co-circulation of both subclades – with Limete health zone reporting the most cases of both subclades. Of those samples sequenced, genomic analysis indicated that greater than 60% of mutations in both subclades were consistent with APOBEC3-driven mutations.InterpretationThese data suggest that as of July 2024, MPXV in Kinshasa has undergone an epidemiological shift with sustained human-to-human transmission and co-circulation of two distinct subclades. Additionally, high rates of APOBEC3-driven changes further support this shift towards human-to-human transmission. While sexual-contact transmission cannot be confirmed without further case investigation, these data highlight important changes in mpox dynamics which may better guide mpox mitigation and containment strategies in Kinshasa.RESEARCH IN CONTEXTEvidence before this studyHistorically, human infections with Clade I monkeypox virus (MPXV) have been driven through zoonotic transmission with limited secondary transmission. However, sexual contact-mediated transmission of Clade I MPXV among a small cluster of cases was identified for the first time in Kwango Province, DRC, in mid-2023. We searched PubMed, bioRxiv, and medRxiv for articles published from database inception to 11 November 2024, with no language restrictions, using the terms “mpox, monkeypox, Congo Basin, Clade I, AND outbreak”. All articles were published from 2010, with the majority published from 2022-2024, and included reviews, case reports, and laboratory investigations. Early reports on mpox outbreaks demonstrated that most infections resulted from zoonotic transmission events and the risks of sustained human-to-human transmission were considered to be very low. Assessment of human-to-human transmission of MPXV in the DRC between 1970-1980 and 1981-1986 suggested that there was no evidence for changes in secondary attack rates. This included a study of 93 MPXV-infected individuals who became symptomatic following close contact with mpox patients from 1981-1986 in DRC. Here, 69 cases resulted from transmission during the first virus generation, 19 in the second generation, and five cases in both the third and fourth generation. During the 1996-1997 mpox outbreak in DRC, it was reported that 73% of cases had contact with an mpox patient. A study of Clade I mpox in the Republic of the Congo from April-July 2003 suggested that up to seven sequential virus generations had occurred during the outbreak and was supported by the clustering of cases, uniform intervals of cases, and prior exposure histories of the patients. High secondary attack rates were also reported during an outbreak of Clade I mpox from July-December 2013 in the DRC where transmissions within the community were estimated to be ≥7 virus generations. While these observations suggested potential increased patterns of human-to-human MPXV transmission, these continued to be linked to close, sustained contacts primarily within households and among caregivers. However, the first report of a cluster of mpox cases in DRC linked to sexual contacts in 2023 suggested that intimate contact, including through heterosexual and same-sex contacts, could result in Clade I MPXV transmission. Viral genome sequences isolated from this case cluster demonstrated the highest sequence similarity with a 2022 Clade I MPXV sequence from DRC. Subsequent investigation of surveillance data in South Kivu province, DRC, from September 2023 to January 2024 identified 241 suspected mpox cases that included sustained human-to-human transmission. Among PCR-confirmed mpox cases, the median age was 22 years with 29% of individuals identifying as sex workers. Genomic analysis identified a distinct clade I lineage, named as subclade Ib, with a predominance of APOBEC3 mutations. Rapid geographic expansion of subclade Ib has resulted in introduction of MPXV to multiple neighboring countries for the first time and including sustained chains of virus transmission, most notably in Burundi. Subclade Ia MPXV has undergone rapid and extensive geographic expansion in DRC since 2023. A recent longitudinal analysis of MPXV genomes from 2018-2024 demonstrated that all non-South Kivu Province sequences exhibited high genetic diversity, low incidences of APOBEC3 mutations as compared to subclade Ib, and likely resulted from multiple zoonotic introductions. Collectively, historic mpox case data and recent observations since 2023 have suggested that human mpox cases in DRC have been driven by zoonotic transmissions of subclade Ia and an increasing burden of sustained human-to-human transmissions of subclade Ib in Eastern DRC, with limited disease burden in Kinshasa.Added value of this studyThis investigation demonstrates a shift in the epidemiology of subclade Ia group II MPXV outbreaks, which had previously been typified by multiple independent zoonotic introductions. Epidemiologic analysis indicated two distinct periods for the Kinshasa mpox outbreak - an initial period from August 2023 to June 2024 characterized by sporadic subclade Ia mpox case detections, and a second period from July 2024-October 2024 characterized by co-emergence of both subclade Ia and Ib. The majority of mpox cases were adult males. In contrast to historic observations, children <15 years were not the primary demographic overrepresented among the subclade Ia mpox cases with those aged 16–49 years accounting for 79% of cases in this study. This investigation sequenced samples from mpox-confirmed cases in Kinshasa, DRC, by generating 115 near-complete MPXV genomes accompanied by phylogenomic analysis. Our findings reveal an escalation of the Kinshasa mpox outbreak that includes the establishment of both subclade Ia (Group II) and subclade Ib MPXV. Subclade Ia introductions (n=11 samples belonging to 5 clusters within Group II) into Kinshasa were observed in 2023 and 2024 with limited local transmission chains. In this analysis, we estimate that 63% of mutations in subclade Ia and 66% of mutations in subclade Ib from MPXV genomes collected in Kinshasa were consistent with APOBEC3-driven changes, a hallmark of human-to-human transmission.Implications of all the available evidenceThis study provides critical evidence for a rapid shift in subclade Ia MPXV epidemiology to include more sustained human-to-human transmission. While Clade I mpox cases have historically been linked to zoonotic transmissions, the recent emergence of subclade Ib in Eastern DRC coupled with our observations reported here for subclade Ia further complicate our understanding of Clade I MPXV transmission. These results have important public health implications for regional and international partners given Kinshasa’s role as an international travel hub and as the largest city on the continent. Observations of new sequences from Kwilu, Kwango, and Kongo-Central provinces (subclade Ia), as well as Kasaï, Tanganyika and Tshopo (subclade Ib), linked to Kinshasa genomes further increase concerns regarding the broader risks for subclade Ia expansion, including within sexual networks.