This is an analysis of Ebola virus genome sequences being produced in the field by teams in Sierra Leone and Guinea over the last few months as the epidemic continues in these countries. A total of 145 sequences from Sierra Leone have been produced a consortium from the Wellcome Trust Sanger Centre, the University of Cambridge and Public Health England. A total of 51 sequences from Guinea have been produced by the EMLab/EVIDENT consortium in collaboration with University of Birmingham.
Figure 1 | Time-resolved phylogenetic tree inferred from an alignment of 985 EBOV genomes. Tips coloured in red are from the previous release of WTSI/UoC/PHE genomes, while those in orange are the novel WTSI/UoC/PHE sequences from Sierra Leone. Tips coloured in blue are the novel EMLab-RT sequences from Guinea. Lineages containing the newly-sequenced isolates are highlighted with coloured boxes and labelled A-H for lineages derived from the SL3 lineage, or GUI-1 for the divergent Guinean lineage. Branches are coloured by inferred geographical location: blue for Sierra Leone, green for Guinea, and orange for Liberia.
Methods. All available West African EBOV genomes from GenBank (1-8) were aligned with the novel genome set. Genomes were partitioned into coding regions and intergenic regions, with the coding region further partitioned into the first, second, and third coding positions. To each partition, an HKY+Γ substitution was employed. An uncorrelated lognormal relaxed clock and a Bayesian SkyGrid tree prior were used. A maximum clade credibility tree was constructed from the posterior set of 9,000 trees drawn from an MCMC chain length of 50M states.
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This is interesting. It appears to me that there’s more diversity among the lineages from Sierra Leone than from the other two countries. Is that correct? If so, is that simply a reflection of our sampling bias or is it possible that we have many more transmission chains ongoing in Sierra Leone, whereas transmission chains are more localized in Guinea? (and more so in Liberia).
Also, a lot of endemic circulation going on.
The pattern in Sierra Leone looks like what we would expect as a large epidemic declines - the gradual extinction of diversity that accumulated during the exponential growth. But it didn’t decline to zero so the lineages that persisted then start to accumulate diversity again. Guinea has fewer of these lineages as it was never the peaking epidemic that the SLE and LBR had.
Heatmaps of the number of cases reported by the WHO (left) and the viral genome sampling by all agencies (right). The right hand plot shows the difference in the actual numbers of sequences by location and month to the expected number if distributed proportionally to the case counts.
Plots by @evogytis