2020 Ebola virus disease outbreak in Équateur Province, Democratic Republic of the Congo: a retrospective genomic characterisation

Eddy Kinganda-Lusamaki, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo; TransVIHMI, University of Montpellier, Institut de Recherche pour le Développement, INSERM, Montpellier, France.
Shannon Whitmer, Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
Emmanuel Lokilo-Lofiko, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.
Adrienne Amuri-Aziza, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.
Francisca Muyembe-Mawete, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
Jean Claude Makangara-Cigolo, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
Gerry Makaya, Vysnova Partners, Landover, MD, USA.
Francis Mbuyi, Vysnova Partners, Landover, MD, USA.
Amy Whitesell, Service de Microbiologie, Cliniques Universitaires, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
Ruth Kallay, Emergency Response and Recovery Branch USA, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
Mary Choi, Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
Catherine Pratt, Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA.
Daniel Mukadi-Bamuleka, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
Hugo Kavunga-Membo, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.
Meris Matondo-Kuamfumu, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
Fabrice Mambu-Mbika, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
Richard Ekila-Ifinji, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
Trevor Shoemaker, Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
Miles Stewart, Johns Hopkins University Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA.
Julia Eng, Johns Hopkins University Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA.
Abraham Rajan, Johns Hopkins University Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, USA.
Gnakub N. Soke, Division of Global Health Protection, US Centers for Disease Control and Prevention, Kinshasa, Democratic Republic of the Congo.
Peter N. Fonjungo, Division of Global HIV and Tuberculosis, US Centers for Disease Control and Prevention, Kinshasa, Democratic Republic of the Congo.
John Otokoye Otshudiema, WHO Health Emergencies Programme, WHO, Kinshasa, Democratic Republic of the Congo.
Gervais Léon Folefack, WHO Health Emergencies Programme, WHO, Kinshasa, Democratic Republic of the Congo.
Elisabeth Pukuta-Simbu, Pathogen Genomics Laboratory, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.
Emir Talundzic, Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
Elizabeth Shedroff, Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
Jacques Likofata Bokete, WHO Health Emergencies Programme, WHO, Kinshasa, Democratic Republic of the Congo.
Anaïs Legand, Health Emergencies Programme, WHO, Geneva, Switzerland.
Pierre Formenty, Health Emergencies Programme, WHO, Geneva, Switzerland.
Christopher N. Mores, Global Health Department, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA.

Document Type

Journal Article

Publication Date

2-1-2024

Journal

The Lancet. Microbe

Volume

5

Issue

2

DOI

10.1016/S2666-5247(23)00259-8

Abstract

BACKGROUND: The Democratic Republic of the Congo has had 15 Ebola virus disease (EVD) outbreaks, from 1976 to 2023. On June 1, 2020, the Democratic Republic of the Congo declared an outbreak of EVD in the western Équateur Province (11th outbreak), proximal to the 2018 Tumba and Bikoro outbreak and concurrent with an outbreak in the eastern Nord Kivu Province. In this Article, we assessed whether the 11th outbreak was genetically related to previous or concurrent EVD outbreaks and connected available epidemiological and genetic data to identify sources of possible zoonotic spillover, uncover additional unreported cases of nosocomial transmission, and provide a deeper investigation into the 11th outbreak. METHODS: We analysed epidemiological factors from the 11th EVD outbreak to identify patient characteristics, epidemiological links, and transmission modes to explore virus spread through space, time, and age groups in the Équateur Province, Democratic Republic of the Congo. Trained field investigators and health professionals recorded data on suspected, probable, and confirmed cases, including demographic characteristics, possible exposures, symptom onset and signs and symptoms, and potentially exposed contacts. We used blood samples from individuals who were live suspected cases and oral swabs from individuals who were deceased to diagnose EVD. We applied whole-genome sequencing of 87 available Ebola virus genomes (from 130 individuals with EVD between May 19 and Sept 16, 2020), phylogenetic divergence versus time, and Bayesian reconstruction of phylogenetic trees to calculate viral substitution rates and study viral evolution. We linked the available epidemiological and genetic datasets to conduct a genomic and epidemiological study of the 11th EVD outbreak. FINDINGS: Between May 19 and Sept 16, 2020, 130 EVD (119 confirmed and 11 probable) cases were reported across 13 Équateur Province health zones. The individual identified as the index case reported frequent consumption of bat meat, suggesting the outbreak started due to zoonotic spillover. Sequencing revealed two circulating Ebola virus variants associated with this outbreak-a Mbandaka variant associated with the majority (97%) of cases and a Tumba-like variant with similarity to the ninth EVD outbreak in 2018. The Tumba-like variant exhibited a reduced substitution rate, suggesting transmission from a previous survivor of EVD. INTERPRETATION: Integrating genetic and epidemiological data allowed for investigative fact-checking and verified patient-reported sources of possible zoonotic spillover. These results demonstrate that rapid genetic sequencing combined with epidemiological data can inform responders of the mechanisms of viral spread, uncover novel transmission modes, and provide a deeper understanding of the outbreak, which is ultimately needed for infection prevention and control during outbreaks. FUNDING: WHO and US Centers for Disease Control and Prevention.

Department

Global Health

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