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.

The genomic data were invaluable in revealing what was happening to the virus during the outbreak, but it would have been even more informative had samples been of uniformly high quality. Many samples did not produce whole-genome assemblies because of poor sample quality, and a third of those that did could not be used to detect iSNVs. This highlights the importance of rapid sequencing in clinical settings during outbreaks, with well-established sample collection and processing protocols. Although at the time of the outbreak sequencing was not yet ready on site, sequencing capability is now becoming increasingly available throughout many regions. With highthroughput deep sequencing now being routinely performed by ACEGID at RUN, high-resolution pathogen information can now be generated to elucidate outbreak dynamics and response, both in Nigeria and throughout West Africa.