Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo
On August 1, 2018, the Democratic Republic of the Congo declared its tenth Ebola virus disease outbreak. To aid the epidemiologic response, the Institut National de Recherche Biomédicale implemented an end-to-end genomic surveillance system, including sequencing, bioinformatic analysis, and dissemination of genomic epidemiologic results to frontline public health workers. We report 744 new genomes sampled between July 27, 2018 and April 27, 2020 generated by this surveillance effort. Together with previously available sequence data (n = 48 genomes), these data represent almost 24% of all laboratory-confirmed Ebola virus infections in DRC in the analyzed period. We inferred spatiotemporal transmission dynamics from the genomic data as new sequences were generated and disseminated the results to support epidemiologic response efforts. Here, we provide an overview of how this genomic surveillance system functioned, present a full phylodynamic analysis of 792 Ebola genomes from the Nord Kivu outbreak, and discuss how the genomic surveillance data informed response efforts and public health decision-making.