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. 2016 Oct 15;214(suppl 3):S102-S109.
doi: 10.1093/infdis/jiw190. Epub 2016 Jul 4.

Ebola Virus Epidemiology and Evolution in Nigeria

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Free PMC article

Ebola Virus Epidemiology and Evolution in Nigeria

Onikepe A Folarin et al. J Infect Dis. .
Free PMC article

Abstract

Containment limited the 2014 Nigerian Ebola virus (EBOV) disease outbreak to 20 reported cases and 8 fatalities. We present here clinical data and contact information for at least 19 case patients, and full-length EBOV genome sequences for 12 of the 20. The detailed contact data permits nearly complete reconstruction of the transmission tree for the outbreak. The EBOV genomic data are consistent with that tree. It confirms that there was a single source for the Nigerian infections, shows that the Nigerian EBOV lineage nests within a lineage previously seen in Liberia but is genetically distinct from it, and supports the conclusion that transmission from Nigeria to elsewhere did not occur.

Keywords: Ebola; Nigeria; epidemiology; genomic; outbreak; phylogeny; sequencing.

Figures

Figure 1.
Figure 1.
Maximum likelihood tree. Phylogenetic analysis confirms a single introduction of Ebola virus into Nigeria from Liberia and places all Nigerian sequences as descendents of Liberia sublineage 5. Two Liberia sublineage genomes (accession Nos. KT725314 and KT725261) cluster closely with Nigerian samples owing to a shared variant at position 18 754. (Scale bar indicates nucleotide substitutions per site.)
Figure 2.
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.

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