Operationalizing genomic epidemiology during the Nord-Kivu Ebola outbreak, Democratic Republic of the Congo

Kinganda-Lusamaki E, Black A, Mukadi D, Hadfield J, Mbala-Kingebeni P, Pratt C, Aziza A, Diagne M, White B, Bisento N, Nsunda B, Akonga M, Faye M, Faye O, Edidi-Atani F, Matondo M, Mambu F, Bulabula J, Di Paola N, Palacios G, Delaporte E, Sall AA, Peeters M, Wiley M, Ahuka-Mundeke S, Bedford T, Muyembe-Tamfum J-J. 2020. medRxiv: 2020.06.08.20125567.

Abstract

The Democratic Republic of the Congo declared its tenth Ebola virus disease outbreak in July 2018, which has circulated primarily in the Nord Kivu province. In addition to standard epidemiologic surveillance and response efforts, the Institut National de Recherche Biom├ędicale implemented an end-to-end genomic surveillance system, including sequencing, bioinformatic analysis, and dissemination of genomic epidemiologic results to frontline public health workers. Here we report 538 new genomes from this outbreak; together with previously available sequence data (n = 48 genomes), this represents an unprecedented 17% of all laboratory-confirmed infections. To support outbreak response efforts, we reconstructed spatiotemporal transmission dynamics at broad and at fine scales as new data were available and disseminated the results via an interactive narrative-based platform. Our innovative system enables actionable information sharing between scientists and epidemiologists coordinating the day-to-day response on the time scales necessary to guide response efforts. The development of this genomic surveillance pipeline, within a resource-limited setting, represents significant technological and scientific progress in genomic epidemiology. Here we present a phylodynamic analysis of the outbreak as of February 2020, and describe the types of epidemiologic dynamics that we monitor the genomic data for, including resolution of co-circulating transmission chains, detection of superspreading events, inference of regions that act as transmission sources and sinks, and differentiation of closely linked cases versus propagated transmission. These findings have ameliorated the current outbreak response and are directly applicable to future outbreaks.