##Genomic Epidemiology of Ebola virus Makona

The following publicly available EBOV Makona genomes from outside of Sierra Leone do not carry the SL3-derived allele at position 10,218: 26 available genomes from Liberia (25 from \citet{Kugelman_2015}, 1 from GenBank KP178538.1) and all 4 available genomes from Mali \citep{Hoenen_2015}. A median-joining haplotype network was constructed in PopART version 1.7.2 (http://popart.otago.ac.nz). Due to the presence of missing data, 1,492 sites (7.9% of total genome) were excluded from the analysis; these sites included 61 sites with variability among isolates (10.9% of all variable sites).

To reconstruct the EBOV Makona transmission history within Sierra Leone, we grouped samples into sets of one or more genetically identical viruses based on their consensus sequences. We then identified relationships between these groups, progressing from the Guinean reference genome (KJ660346.2) and ending with nine viruses sampled in Freetown (eight from our KGH and CDC cohorts and one sequenced in Italy).