Blood samples were collected from 78 patients at Kenema Government Hospital in Sierra Leone. For details of RNA preservation, PCR, human RNA depletion, library construction and sequencing, see Supplemental Materials and Methods of Gire et al.
Gire et al. analyzed the 78 Sierra Leone patient sequences together with 3 sequences from the 2014 outbreak in Guinea (Baize et al.; suspected sequencing errors were masked, see Supplemental Materials and Methods of Gire et al.), for a total of 81 sequences from 2014. In addition, some analyses included 20 sequences from past outbreaks of Zaire Ebola virus, 1976-2008, for a total of 101 sequences. Sequence variants were extracted directly from multiple sequence alignments of the group of 101 sequences (1976-2014). A custom release of -SnpEff +SnpEff (v4.0, build 2014-07-01, to support ribosomal slippage in transcription of GP gene) was used to predict functional effect of variants on genes (noncoding, synonymous or missense).