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.

Identifying individual links in the transmission chain is usually beyond the resolution of sequence data, however, and requires contact tracing in the field. The resolution of genomic data is limited because new variants arise less often than new cases, meaning that many cases will be genetically indistinguishable. This can be seen Figure 2 . Transmission tree. A, Transmission reconstructed from of Ebola virus genome sequence and sample dates only. Arrows indicate likely transmission; cases not connected to arrows cannot be placed within the transmission tree given the available data. LB5, Liberia sublineage 5 reference. B, Transmission reconstructed from contact tracing only. Contact tracing provides more precise information, but is not always available. Samples were collected in Lagos, Nigeria, unless otherwise identified. Each case is labeled with its sample collection date; cases not connected to sequenced samples are labeled with date of hospitalization. Samples are colored by consensus sequence (ie, samples with identical viral genomes are similarly colored). Cases in gray are those for which genetic data are not available. Abbreviation: SNPs, single-nucleotide polymorphisms.