Author: 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.
Title: Ebola Virus Epidemiology and Evolution in Nigeria Document date: 2016_10_15
ID: 2g9ggwog_48
Snippet: Also puzzling is a pair of variants that were seen twice, once as consensus SNPs (in case 9) and once as iSNVs (in case 6). Based on sample dates and contact data, both of these patients were infected by the index patient, so presumably they inherited these variants from that patient. We do not, however, find them in the sample from the index patients, either as consensus SNPs or as iSNVs, despite high sequencing depth. Nor do they appear as cons.....
Document: Also puzzling is a pair of variants that were seen twice, once as consensus SNPs (in case 9) and once as iSNVs (in case 6). Based on sample dates and contact data, both of these patients were infected by the index patient, so presumably they inherited these variants from that patient. We do not, however, find them in the sample from the index patients, either as consensus SNPs or as iSNVs, despite high sequencing depth. Nor do they appear as consensus SNPs in the other cases derived from the index case, or as iSNVs in the one other case that was deeply sequenced and was sampled around the same time as samples 6 and 9. The explanation may simply be that the variants were present in the index patient but at too low a frequency for us to detect. It is also possible that their frequency changed in the index patient between the time he was sampled and transmission to the other cases, or that they differed across tissues within the patient. Better understanding of the dynamics of within-host evolution and transmission, and of our power to detect iSNVs, would help clarify this issue.
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