Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

Armando Arias, Simon J. Watson, Danny Asogun, Ekaete Alice Tobin, Jia Lu, My V.T. Phan, Umaru Jah, Raoul Emeric Guetiya Wadoum, Luke Meredith, Lucy Thorne, Sarah Caddy, Alimamy Tarawalie, Pinky Langat, Gytis Dudas, Nuno R. Faria, Simon Dellicour, Abdul Kamara, Brima Kargbo, Brima Osaio Kamara, Sahr GevaoDaniel Cooper, Matthew Newport, Peter Horby, William Dunning, Foday Sahr, Timothy Brooks, Andrew Simpson, Elisabetta Groppelli, Guoying Liu, Nisha Mulakken, Kate Rhodes, James Akpablie, Zabulon Yoti, Margaret Lamunu, Esther Vitto, Patrick Otim, Collins Owilli, Isaac Boateng, Lawrence Okoror, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Ighodalo Yemisis, Donatus Adomeh, Solomon Ehikhiametalor, Patience Akhilomen, Chris Aire, Andreas Kurth, Nicola Cook, Jan Baumann, Martin Gabriel, Roman Wölfel, Antonino Di Caro, Miles Carroll, Stephan Günther, John Redd, Dhamari Naidoo, Oliver G. Pybus, Andrew Rambaut, Paul Kellam, Ian Goodfellow*, Matthew Cotten

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

91 Citations (Scopus)


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.

Original languageEnglish
Article numbervew016
JournalVirus Evolution
Issue number1
Publication statusPublished - Jan 2016

Bibliographical note

Publisher Copyright:
© The Author, 2016.


  • Ebola virus
  • evolution
  • outbreak sequencing.
  • transmission


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