Placide Mbala-Kingebeni1, Catherine B Pratt2, Michael R Wiley2, Moussa M Diagne3, Sheila Makiala-Mandanda4, Amuri Aziza5, Nicholas Di Paola6, Joseph A Chitty6, Mamadou Diop3, Ahidjo Ayouba7, Nicole Vidal7, Ousmane Faye3, Oumar Faye3, Stormy Karhemere5, Aaron Aruna8, Justus Nsio8, Felix Mulangu8, Daniel Mukadi9, Patrick Mukadi5, John Kombe8, Anastasie Mulumba10, Sophie Duraffour11, Jacques Likofata12, Elisabeth Pukuta5, Katie Caviness6, Maggie L Bartlett13, Jeanette Gonzalez6, Timothy Minogue14, Shanmuga Sozhamannan15, Stephen M Gross16, Gary P Schroth16, Jens H Kuhn17, Eric F Donaldson18, Eric Delaporte7, Mariano Sanchez-Lockhart13, Martine Peeters7, Jean-Jacques Muyembe-Tamfum4, Amadou Alpha Sall3, Gustavo Palacios19, Steve Ahuka-Mundeke20. 1. Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo. 2. Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA. 3. Institut Pasteur de Dakar, Dakar, Senegal. 4. Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo. 5. Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo. 6. Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA. 7. TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France. 8. Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo. 9. Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo. 10. Monsieur le Représentant de l'Organisation Mondiale de la Santé, Democratic Republic of the Congo. 11. Monsieur le Représentant de l'Organisation Mondiale de la Santé, Democratic Republic of the Congo; Bernhard-Nocht-Institut für Tropenmedizin, Hamburg, Germany. 12. Laboratoire Provinciale, Mbandaka, Democratic Republic of the Congo. 13. Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA. 14. Diagnostics Services Division, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA. 15. Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense-Joint Project Management Office for Guardian, Frederick, MD, USA; Logistics Management Institute, Tysons, VA, USA. 16. Illumina, San Diego, CA, USA. 17. Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA. 18. Division of Antiviral Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA. 19. Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA. Electronic address: gustavo.f.palacios.civ@mail.mil. 20. Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo; Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.
Abstract
BACKGROUND: The 2018 Ebola virus disease (EVD) outbreak in Équateur Province, Democratic Republic of the Congo, began on May 8, and was declared over on July 24; it resulted in 54 documented cases and 33 deaths. We did a retrospective genomic characterisation of the outbreak and assessed potential therapeutic agents and vaccine (medical countermeasures). METHODS: We used target-enrichment sequencing to produce Ebola virus genomes from samples obtained in the 2018 Équateur Province outbreak. Combining these genomes with genomes associated with known outbreaks from GenBank, we constructed a maximum-likelihood phylogenetic tree. In-silico analyses were used to assess potential mismatches between the outbreak strain and the probes and primers of diagnostic assays and the antigenic sites of the experimental rVSVΔG-ZEBOV-GP vaccine and therapeutics. An in-vitro flow cytometry assay was used to assess the binding capability of the individual components of the monoclonal antibody cocktail ZMapp. FINDINGS: A targeted sequencing approach produced 16 near-complete genomes. Phylogenetic analysis of these genomes and 1011 genomes from GenBank revealed a distinct cluster, confirming a new Ebola virus variant, for which we propose the name "Tumba". This new variant appears to have evolved at a slower rate than other Ebola virus variants (0·69 × 10-3 substitutions per site per year with "Tumba" vs 1·06 × 10-3 substitutions per site per year without "Tumba"). We found few sequence mismatches in the assessed assay target regions and antigenic sites. We identified nine amino acid changes in the Ebola virus surface glycoprotein, of which one resulted in reduced binding of the 13C6 antibody within the ZMapp cocktail. INTERPRETATION: Retrospectively, we show the feasibility of using genomics to rapidly characterise a new Ebola virus variant within the timeframe of an outbreak. Phylogenetic analysis provides further indications that these variants are evolving at differing rates. Rapid in-silico analyses can direct in-vitro experiments to quickly assess medical countermeasures. FUNDING: Defense Biological Product Assurance Office.
BACKGROUND: The 2018 Ebola virus disease (EVD) outbreak in Équateur Province, Democratic Republic of the Congo, began on May 8, and was declared over on July 24; it resulted in 54 documented cases and 33 deaths. We did a retrospective genomic characterisation of the outbreak and assessed potential therapeutic agents and vaccine (medical countermeasures). METHODS: We used target-enrichment sequencing to produce Ebola virus genomes from samples obtained in the 2018 Équateur Province outbreak. Combining these genomes with genomes associated with known outbreaks from GenBank, we constructed a maximum-likelihood phylogenetic tree. In-silico analyses were used to assess potential mismatches between the outbreak strain and the probes and primers of diagnostic assays and the antigenic sites of the experimental rVSVΔG-ZEBOV-GP vaccine and therapeutics. An in-vitro flow cytometry assay was used to assess the binding capability of the individual components of the monoclonal antibody cocktail ZMapp. FINDINGS: A targeted sequencing approach produced 16 near-complete genomes. Phylogenetic analysis of these genomes and 1011 genomes from GenBank revealed a distinct cluster, confirming a new Ebola virus variant, for which we propose the name "Tumba". This new variant appears to have evolved at a slower rate than other Ebola virus variants (0·69 × 10-3 substitutions per site per year with "Tumba" vs 1·06 × 10-3 substitutions per site per year without "Tumba"). We found few sequence mismatches in the assessed assay target regions and antigenic sites. We identified nine amino acid changes in the Ebola virus surface glycoprotein, of which one resulted in reduced binding of the 13C6 antibody within the ZMapp cocktail. INTERPRETATION: Retrospectively, we show the feasibility of using genomics to rapidly characterise a new Ebola virus variant within the timeframe of an outbreak. Phylogenetic analysis provides further indications that these variants are evolving at differing rates. Rapid in-silico analyses can direct in-vitro experiments to quickly assess medical countermeasures. FUNDING: Defense Biological Product Assurance Office.
Authors: Alpha Kabinet Keita; Fara R Koundouno; Martin Faye; Ariane Düx; Julia Hinzmann; Haby Diallo; Ahidjo Ayouba; Frederic Le Marcis; Barré Soropogui; Kékoura Ifono; Moussa M Diagne; Mamadou S Sow; Joseph A Bore; Sebastien Calvignac-Spencer; Nicole Vidal; Jacob Camara; Mamadou B Keita; Annick Renevey; Amadou Diallo; Abdoul K Soumah; Saa L Millimono; Almudena Mari-Saez; Mamadou Diop; Ahmadou Doré; Fodé Y Soumah; Kaka Kourouma; Nathalie J Vielle; Cheikh Loucoubar; Ibrahima Camara; Karifa Kourouma; Giuditta Annibaldis; Assaïtou Bah; Anke Thielebein; Meike Pahlmann; Steven T Pullan; Miles W Carroll; Joshua Quick; Pierre Formenty; Anais Legand; Karla Pietro; Michael R Wiley; Noel Tordo; Christophe Peyrefitte; John T McCrone; Andrew Rambaut; Youssouf Sidibé; Mamadou D Barry; Madeleine Kourouma; Cé D Saouromou; Mamadou Condé; Moussa Baldé; Moriba Povogui; Sakoba Keita; Mandiou Diakite; Mamadou S Bah; Amadou Sidibe; Dembo Diakite; Fodé B Sako; Fodé A Traore; Georges A Ki-Zerbo; Philippe Lemey; Stephan Günther; Liana E Kafetzopoulou; Amadou A Sall; Eric Delaporte; Sophie Duraffour; Ousmane Faye; Fabian H Leendertz; Martine Peeters; Abdoulaye Toure; N' Faly Magassouba Journal: Nature Date: 2021-09-15 Impact factor: 49.962
Authors: Brien K Haun; Varney Kamara; Abigail S Dweh; Kianalei Garalde-Machida; Saymajunkon S E Forkay; Melissa Takaaze; Madhuri Namekar; Teri Ann S Wong; Ayesha E R Bell-Gam Woto; Peter Humphreys; Ophelia I Weeks; Mosoka P Fallah; John M Berestecky; Vivek R Nerurkar; Axel T Lehrer Journal: PLoS Negl Trop Dis Date: 2019-07-22
Authors: David J Pascall; Kyriaki Nomikou; Emmanuel Bréard; Stephan Zientara; Ana da Silva Filipe; Bernd Hoffmann; Maude Jacquot; Joshua B Singer; Kris De Clercq; Anette Bøtner; Corinne Sailleau; Cyril Viarouge; Carrie Batten; Giantonella Puggioni; Ciriaco Ligios; Giovanni Savini; Piet A van Rijn; Peter P C Mertens; Roman Biek; Massimo Palmarini Journal: PLoS Biol Date: 2020-04-28 Impact factor: 8.029
Authors: Andrew Bosworth; Natasha Y Rickett; Xiaofeng Dong; Lisa F P Ng; Isabel García-Dorival; David A Matthews; Tom Fletcher; Michael Jacobs; Emma C Thomson; Miles W Carroll; Julian A Hiscox Journal: Genome Med Date: 2021-01-11 Impact factor: 11.117
Authors: Shevin T Jacob; Ian Crozier; William A Fischer; Angela Hewlett; Colleen S Kraft; Marc-Antoine de La Vega; Moses J Soka; Victoria Wahl; Anthony Griffiths; Laura Bollinger; Jens H Kuhn Journal: Nat Rev Dis Primers Date: 2020-02-20 Impact factor: 52.329
Authors: Jill R Wells; Ian Crozier; Colleen S Kraft; Mary Elizabeth Sexton; Charles E Hill; Bruce S Ribner; Sina Bavari; Gustavo Palacios; William A Pearce; Russell Van Gelder; Hans Grossniklaus; Lisa Cazares; Xiankun Zeng; Jessica G Shantha; Steven Yeh Journal: Emerg Infect Dis Date: 2020-07 Impact factor: 6.883
Authors: Kayla G Barnes; Anna E Lachenauer; Adam Nitido; Sameed Siddiqui; Robin Gross; Brett Beitzel; Katherine J Siddle; Catherine A Freije; Bonnie Dighero-Kemp; Samar B Mehta; Amber Carter; Jessica Uwanibe; Fehintola Ajogbasile; Testimony Olumade; Ikponmwosa Odia; John Demby Sandi; Mambu Momoh; Hayden C Metsky; Chloe K Boehm; Aaron E Lin; Molly Kemball; Daniel J Park; Luis Branco; Matt Boisen; Brian Sullivan; Mihret F Amare; Abdulwasiu B Tiamiyu; Zahra F Parker; Michael Iroezindu; Donald S Grant; Kayvon Modjarrad; Cameron Myhrvold; Robert F Garry; Gustavo Palacios; Lisa E Hensley; Stephen F Schaffner; Christian T Happi; Andres Colubri; Pardis C Sabeti Journal: Nat Commun Date: 2020-08-17 Impact factor: 14.919