Genotypic anomaly in Ebola virus strains circulating in Magazine Wharf area, Freetown, Sierra Leone, 2015

In Sierra Leone, two new Ebola virus (EBOV) cases were reported from the densely populated Magazine Wharf area of Freetown in the Western Area Urban district after a period of two weeks in June 2015 with no cases in the district. The Magazine Wharf area was subsequently a focus of transmission for several weeks (http://apps.who.int/ebola/current-situation/ebola-situation-report-15-july-2015) up to 12 August 2015 (http://apps.who.int/ebola/current-situation/ebola-situation-report-12-august-2015), after which no new cases were reported from the area (http://apps.who.int/ebola/current-situation/ebola-situation-report-30-september-2015). In this study, the whole genomes of viruses from patient samples, originating from the Western Area Urban district and other districts of the country (i.e. Kenema, Kono, and Tonkolili) between January and July 2015 are sequenced. Genomes derived from samples collected from 30 June onwards in the Western Area Urban district have a particular anomaly consisting of a series of 13 T to C substitutions in a 150 bp intergenic region downstream of the viral protein 40 (VP40) open reading frame (ORF). This anomaly is also present in a viral strain, the Ebolavirus/H.sapiens-wt/SLE/2014/Makona-J0169 (J0169), which was detected in Freetown in November 2014. The finding suggests that viruses retrieved in June and July 2015 from the Western Area Urban district are direct descendants of a J0169-like virus. Near real time application of whole EBOV genome sequencing and the identification of lineage signatures can be used to monitor the ongoing outbreak and test whether newly infected patients are part of an identified transmission chain.