2020 Ebola virus disease outbreak in Équateur Province, Democratic Republic of the Congo: a retrospective genomic characterisation
Authors: Eddy Kinganda-Lusamaki, Shannon Whitmer, Emmanuel Lokilo-Lofiko, Adrienne Amuri-Aziza, Francisca Muyembe-Mawete, Jean Claude Makangara-Cigolo, Gerry Makaya, Francis Mbuyi, Amy Whitesell, Ruth Kallay, Mary Choi, Catherine Pratt, Daniel Mukadi-Bamuleka, Hugo Kavunga-Membo, Meris Matondo-Kuamfumu, Fabrice Mambu-Mbika, Richard Ekila-Ifinji, Trevor Shoemaker, Miles Stewart, Julia Eng, Abraham Rajan, Gnakub N Soke, Peter N Fonjungo, John Otokoye Otshudiema, Gervais Léon Tengomo Folefack, Elisabeth Pukuta-Simbu, Emir Talundzic, Elizabeth Shedroff, Jacques Likofata Bokete, Anaïs Legand, Pierre Formenty, Christopher N Mores, Abigail J Porzucek, Sarah R Tritsch, John Kombe, Gaston Tshapenda, Felix Mulangu, Ahidjo Ayouba, Eric Delaporte, Martine Peeters, Michael R Wiley, Joel M Montgomery, John D Klena, Jean-Jacques Muyembe-Tamfum, Steve Ahuka-Mundeke, Placide Mbala-Kingebeni
Journal: The Lancet Microbe (2024)

BackgroundThe 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.MethodsWe 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.FindingsBetween 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.InterpretationIntegrating 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.FundingWHO and US Centers for Disease Control and Prevention.