Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo
Eddy Kinganda-Lusamaki
(1, 2)
,
Allison Black
(3, 4)
,
Daniel Mukadi
(1)
,
James Hadfield
(4)
,
Placide Mbala-Kingebeni
(2, 1)
,
Catherine Pratt
(5)
,
Amuri Aziza
(2)
,
Moussa M Diagne
(6)
,
Bailey White
(5)
,
Nella Bisento
(2)
,
Bibiche Nsunda
(2)
,
Marceline Akonga
(2)
,
Martin Faye
(6, 7)
,
Ousmane Faye
(6, 7)
,
François Edidi-Atani
(2, 1)
,
Meris Matondo-Kuamfumu
(2, 1)
,
Fabrice Mambu-Mbika
(2, 1)
,
Junior Bulabula
(2, 1)
,
Nicholas Di Paola
,
Matthias Pauthner
(8)
,
Kristian Andersen
(8)
,
Gustavo Palacios
,
Eric Delaporte
(9, 10)
,
Amadou Alpha Sall
(6)
,
Martine Peeters
(10, 9)
,
Michael Wiley
(5)
,
Steve Ahuka-Mundeke
(1, 2)
,
Trevor Bedford
(3, 4)
,
Jean-Jacques Muyembe Tamfum
(1, 2)
1
UNIKIN -
University of Kinshasa
2 INRB - Institut National de Recherche Biomédicale [Kinshasa]
3 University of Washington [Seattle]
4 FHCRC - Fred Hutchinson Cancer Research Center [Seattle]
5 University of Nebraska Medical Center
6 Institut Pasteur de Dakar
7 UCAD - Université Cheikh Anta Diop de Dakar [Sénégal]
8 The Scripps Research Institute [La Jolla, San Diego]
9 TransVIHMI - Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes
10 CHRU Montpellier - Centre Hospitalier Régional Universitaire [Montpellier]
2 INRB - Institut National de Recherche Biomédicale [Kinshasa]
3 University of Washington [Seattle]
4 FHCRC - Fred Hutchinson Cancer Research Center [Seattle]
5 University of Nebraska Medical Center
6 Institut Pasteur de Dakar
7 UCAD - Université Cheikh Anta Diop de Dakar [Sénégal]
8 The Scripps Research Institute [La Jolla, San Diego]
9 TransVIHMI - Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes
10 CHRU Montpellier - Centre Hospitalier Régional Universitaire [Montpellier]
Allison Black
- Fonction : Auteur
- PersonId : 798819
- ORCID : 0000-0002-6618-4127
Catherine Pratt
- Fonction : Auteur
- PersonId : 822763
- ORCID : 0000-0001-6132-2570
Nicholas Di Paola
- Fonction : Auteur
Matthias Pauthner
- Fonction : Auteur
- PersonId : 782046
- ORCID : 0000-0001-9212-4307
Gustavo Palacios
- Fonction : Auteur
- PersonId : 771122
- ORCID : 0000-0001-5062-1938
Résumé
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 Biomédicale (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.