##Sample Preparation from Kenema Government Hospital
This study included 575 blood samples from 84 patients with confirmed EVD from June 16 through September 28, 2014 by KGH laboratory staff. Clinical samples were inactivated using Qiagen AVL and ethanol in the KGH laboratory prior to shipping out of the country.

##Sample Preparation from CDC Bo Laboratory
This study included 98 blood samples from 98 patients with confirmed EVD from August 20, 2014 through January 10, 2015 by CDC laboratory staff stationed in Bo, Sierra Leone. Clinical specimens from the CDC Bo laboratory in Sierra Leone were shipped to and stored at the Viral Special Pathogens Branch BSL-4 laboratory at CDC in Atlanta, GA. Samples were inactivated, and RNA was extracted using the MagMAX Pathogen RNA/DNA isolation kit (Invitrogen) and BeadRetriever (Invitrogen). Non-infectious RNA was treated with DNase I RNase-free (Roche) prior to shipment to the Broad Institute.

##High-throughput Sequencing
Host ribosomal and carrier poly(rA) RNA depletion, randomly-primed cDNA synthesis, Nextera XT library construction and 101-bp paired-end Illumina sequencing were performed as described previously \citep{Gire_2014, Matranga_2014}.