Recent evolution patterns of Ebola virus obtained by direct sequencing in Sierra Leone

EBOV_genome_release_2Jul15.pdf (90.1 KB)

Recent evolution patterns of Ebola virus from December 2014-June 2015 obtained by direct sequencing in Sierra Leone.

Ian Goodfellow a, Armando Arias a, Sarah Caddy a, Lucy Thorne a, Brima Kargbo b, Brima Osaio Kamara b, Umaru Jah c, Daniel Cooper c, Matthew Newport c, Rosanda Working Group, Peter Horby d, Tim Brooks e, Andrew Simpson e, Simon J. Watson f, Pinky Langat f, My V.T. Phan f, Matthew Cotten f, Andrew Rambaut g,h, Paul Kellam f,i,

a. Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
b. Sierra Leone Ministry of Health, Freetown, Sierra Leone
c. International Medical Corps
d. University of Oxford, Oxford, United Kingdom
e. Public Health England
f. Wellcome Trust Sanger Institute, Hinxton, United Kingdom
g. Institute of Evolutionary Biology, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh, United Kingdom
h. Fogarty International Center, NIH, Bethesda, Maryland, USA
i. Division of Infection and Immunity, University College London, London, United Kingdom

In a collaborative effort between the University of Cambridge, Public Health England, and the Wellcome Trust Sanger Institute, with the support of the Sierra Leone Ministry of Health, International Medical Corps, DfID, Thermo and the Wellcome Trust, we are monitoring the evolution and transmission patterns of Ebola virus (EBOV) .thin Sierra Leone.

We have continued our efforts to provide full genome EBOV sequences for monitoring the outbreak in Sierra Leone (1). The local sequencing facility established at the Mateneh Ebola Treatment Centre in Makeni, Bombali district, Sierra Leone has continued to sequence EBOV genomes with immediate on-site extraction, processing and deep sequencing of EBOV-positive patient samples(1). As previously described, the short read data were electronically transferred to computer facilities in the UK for assembly into viral genomes. An additional 74 EBOV genomes were obtained from samples collected between 2 December 2014 and 9 June 2015. An alignment of the 74 new EBOV genome sequences and the entire set of 145 EBOV genomes from this study are available at the following link:

Disclaimer. We make these sequence data publically available with the hope that they are useful for other scientists and the caveat that they are preliminary and still undergoing quality control. A manuscript analyzing the phylogenetic patterns in more detail is in preparation. If investigators would like to use these sequence data for publication prior to release of our paper, please contact us.

Methods | Patients were from clinics in Makeni (Bombali District), Port Loko, Kambia, Western Urban district and Koinadugu. PCR positive samples were subjected to reverse transcription/PCR amplification using the Thermo Ampliseq workflow with EBOV specific reagents and the Ion Torrent sequencing platform. The resultant short reads were quality controlled (length >125 nt, median Phred score > 30) and assembled using the SPAdes 3.5.0 de novo algorithm (2) with Ion Torrent settings, the resulting contigs were sorted and assembled into complete genomes with conflicts resolved by direct counting of short reads.

Summary | Molecular clock phylogenies of the EBOV outbreak reveal that in April 2015 there were at least 5 separate transmission chains maintained within Sierra Leone (Figure 1). However, by June 2015 the number of chains had apparently been reduced to only a single lineage (F), isolated from patients in Port Loko. Viruses from this lineage were derived from Kambia and the western districts of Sierra Leone, and have since been circulating in Port Loko for at least a month. The presence of many long branches in the phylogeny suggests a number of transmission chains that are not sampled through the current surveillance efforts. Additional phylogenetic analysis of all available EBOV genomes can be found at the following link:


  1. Goodfellow I, Arias A, Caddy S, Kargbo B, Osaio Kamara B, Jah U, Cooper D, Newport M, Group RW, Horby P, Brooks T, Simpson A, Cotten M, Watson SJ, Rambaut A, Kellam P. 2015. Recent evolution patterns of Ebola virus inferred from patient samples collected from February-May 2015 with direct deep sequencing in Sierra Leone. http://wwwvirologicalorg/t/direct-deep-sequencing-in-sierra-leone- yields-73-new-ebov-genomes-from-february-may-2015/134.
  2. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455-477.