Ebola Virus Epidemiology and Evolution in Nigeria

Folarin, Onikepe A.; Ehichioya, Deborah; Schaffner, Stephen F.; Winnicki, Sarah M.; Wohl, Shirlee; Eromon, Philomena; West, Kendra L.; Gladden-Young, Adrianne; Oyejide, Nicholas E.; Matranga, Christian B.; Deme, Awa Bineta; James, Ayorinde; Tomkins-Tinch, Christopher; Onyewurunwa, Kenneth; Ladner, Jason T.; Palacios, Gustavo; Nosamiefan, Iguosadolo; Andersen, Kristian G.; Omilabu, Sunday; Park, Daniel J.; Yozwiak, Nathan L.; Nasidi, Abdusallam; Garry, Robert F.; Tomori, Oyewale; Sabeti, Pardis C.; Happi, Christian T.

Extracted RNA samples contained an average of 3.97 × 10 6 18S copies/mL (range, 3.28 × 10 4 to 2.31 × 10 7 copies/mL) as determined by qRT-PCR. We prepared Nextera libraries for all 32 samples. Using the Kulesh qRT-PCR assay, we detected EBOV RNA in 18 of these samples, including 2 discharge samples and 3 samples unassociated with a particular case. After library construction, we used Kulesh qPCR to detect the presence of any EBOV copies in the libraries. Based on the results, we sequenced 23 samples using a combination of the MiSeq and HiSeq 2500 platforms (Illumina). We were able to generate assembled EBOV genomes from 12 of these samples, all from confirmed EVD cases with associated case histories. We combined the MiSeq and HiSeq sequencing data from RUN and the Broad Institute for analysis. The median sequencing coverage was 225.5× (range, 6-4864×) ( Table 1 ). Although we recorded combined sequencing data, the MiSeq data from RUN separately confirmed EBOV reads in 6 of the 12 samples with assembled EBOV genomes.