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Arias A, Watson SJ, Asogun D, Tobin EA, Lu J, Phan MVT, Jah U, Wadoum REG, Meredith L, Thorne L, Caddy S, Tarawalie A, Langat P, Dudas G, Faria NR, Dellicour S, Kamara A, Kargbo B, Kamara BO, Gevao S, Cooper D, Newport M, Horby P, Dunning J, Sahr F, Brooks T, Simpson AJH, Groppelli E, Liu G, Mulakken N, Rhodes K, Akpablie J, Yoti Z, Lamunu M, Vitto E, Otim P, Owilli C, Boateng I, Okoror L, Omomoh E, Oyakhilome J, Omiunu R, Yemisis I, Adomeh D, Ehikhiametalor S, Akhilomen P, Aire C, Kurth A, Cook N, Baumann J, Gabriel M, Wölfel R, Di Caro A, Carroll MW, Günther S, Redd J, Naidoo D, Pybus OG, Rambaut A, Kellam P, Goodfellow I, Cotten M. Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evol 2016; 2:vew016. [PMID: 28694998 PMCID: PMC5499387 DOI: 10.1093/ve/vew016] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts.
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Affiliation(s)
- Armando Arias
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Simon J Watson
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Danny Asogun
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ekaete Alice Tobin
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jia Lu
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - My V T Phan
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Umaru Jah
- University of Makeni, Makeni, Sierra Leone
| | | | - Luke Meredith
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Lucy Thorne
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Caddy
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Pinky Langat
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Gytis Dudas
- Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Abdul Kamara
- Sierra Leone Ministry of Health, Freetown, Sierra Leone
| | - Brima Kargbo
- Sierra Leone Ministry of Health, Freetown, Sierra Leone
| | | | - Sahr Gevao
- Sierra Leone Ministry of Health, Freetown, Sierra Leone
| | | | | | - Peter Horby
- Department of Medicine, Epidemic Diseases Research Group Oxford (ERGO), Centre for Tropical Medicine and Global Health Nuffield, University of Oxford, Oxford, United Kingdom
| | - Jake Dunning
- Department of Medicine, Epidemic Diseases Research Group Oxford (ERGO), Centre for Tropical Medicine and Global Health Nuffield, University of Oxford, Oxford, United Kingdom
| | - Foday Sahr
- Republic of Sierra Leone Armed Forces, Freetown, Sierra Leone
| | - Tim Brooks
- Rare and Imported Pathogens Laboratory, Public Health England, United Kingdom
| | - Andrew J H Simpson
- Rare and Imported Pathogens Laboratory, Public Health England, United Kingdom
| | | | - Guoying Liu
- Thermo Fisher Scientific, South San Francisco, CA, USA
| | | | - Kate Rhodes
- Thermo Fisher Scientific, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | - Emmanuel Omomoh
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jennifer Oyakhilome
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Racheal Omiunu
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ighodalo Yemisis
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Donatus Adomeh
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Solomon Ehikhiametalor
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Patience Akhilomen
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Chris Aire
- Irrua Specialist Teaching Hospital, Institute of Lassa Fever Research and Control, Irrua, Nigeria.,The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Andreas Kurth
- The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Robert Koch Institute, Berlin, Germany
| | - Nicola Cook
- The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Public Health England, Porton Down, United Kingdom
| | - Jan Baumann
- The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Martin Gabriel
- The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Roman Wölfel
- The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Bundeswehr Institute of Microbiology, Munich, Germany
| | - Antonino Di Caro
- The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Miles W Carroll
- The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Public Health England, Porton Down, United Kingdom
| | - Stephan Günther
- The European Mobile Laboratory Consortium, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Redd
- Sierra Leone and Division of Global Health Protection, CDC Country Office, Georgia Center for Global Health Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Andrew Rambaut
- Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom.,Fogarty International Center, NIH, Bethesda, MD, USA.,Infection and Evolution, Centre for Immunology, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom.,University of Makeni, Makeni, Sierra Leone
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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