Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo

Autor: Francois Edidi-Atani, Moussa Moïse Diagne, Meris Matondo-Kuamfumu, Junior Bulabula, Kristian G. Andersen, Bibiche Nsunda, Eric Delaporte, Bailey White, Amadou A. Sall, Trevor Bedford, Matthias Pauthner, Martine Peeters, Nella Bisento, Jean Jacques Muyembe Tamfum, Marceline Akonga, James Hadfield, Daniel Mukadi, Michael R. Wiley, Gustavo Palacios, Fabrice Mambu-Mbika, Amuri Aziza, Nicholas Di Paola, Steve Ahuka-Mundeke, Eddy Kinganda-Lusamaki, Catherine Pratt, Ousmane Faye, Martin Faye, Allison Black, Placide Mbala-Kingebeni
Přispěvatelé: University of Kinshasa (UNIKIN), Institut National de Recherche Biomédicale [Kinshasa] (INRB), University of Washington [Seattle], Fred Hutchinson Cancer Research Center [Seattle] (FHCRC), University of Nebraska Medical Center, University of Nebraska System, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), The Scripps Research Institute [La Jolla, San Diego], Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Retiveau, Nolwenn
Rok vydání: 2021
Předmět:
0301 basic medicine
MESH: Sequence Analysis
DNA
medicine.medical_specialty
Genomic data
MESH: Reinfection
[SDV.BC]Life Sciences [q-bio]/Cellular Biology
Genome
Viral
Disease
medicine.disease_cause
Genome
Article
General Biochemistry
Genetics and Molecular Biology
Disease Outbreaks
03 medical and health sciences
MESH: Spatio-Temporal Analysis
Spatio-Temporal Analysis
0302 clinical medicine
Recurrence
Environmental health
MESH: Congo
[SDV.BBM] Life Sciences [q-bio]/Biochemistry
Molecular Biology
medicine
MESH: Ebola Vaccines
[SDV.BBM]Life Sciences [q-bio]/Biochemistry
Molecular Biology
MESH: Disease Outbreaks
MESH: Ebolavirus
Ebola Vaccines
MESH: Phylogeny
[SDV.BC] Life Sciences [q-bio]/Cellular Biology
Phylogeny
Ebola virus
Transmission (medicine)
MESH: Genomics
Genomic sequencing
Public health
Outbreak
Genomics
Sequence Analysis
DNA
General Medicine
Hemorrhagic Fever
Ebola
Ebolavirus
MESH: Recurrence
030104 developmental biology
Geography
Congo
Reinfection
030220 oncology & carcinogenesis
MESH: Hemorrhagic Fever
Ebola
MESH: Genome
Viral
Zdroj: Nat Med
Nature Medicine
Nature Medicine, 2021, 27 (4), pp.710-716. ⟨10.1038/s41591-021-01302-z⟩
ISSN: 1546-170X
1078-8956
1744-7933
DOI: 10.1038/s41591-021-01302-z
Popis: On 1 August 2018, the Democratic Republic of the Congo (DRC) declared its tenth Ebola virus disease (EVD) outbreak. To aid the epidemiologic response, the Institut National de Recherche Biomedicale (INRB) 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 27 July 2018 and 27 April 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 (EBOV) infections in DRC in the period analyzed. 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. Phylogeographic analysis of 792 Ebola virus genomes from the 2018 oubreak in the Democratic Republic of the Congo integrated into an end-to-end surveillance program demonstrates the feasibility of using genomic sequencing data to inform the public health epidemic response in near-real time.
Databáze: OpenAIRE
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