In further collaboration with Richard Neher, we've released a web-based tool that tracks the ongoing evolution and geographic spread of Ebola virus in West Africa. The tool is available at ebola.nextflu.org and shows a phylogenetic tree of publicly available EBOV sequences along with a map of Guinea, Sierra Leone and Liberia. Mousing over prefectures/districts/counties highlights viruses collected from those regions and vice versa. This makes some geographic connections obvious, like the general East to West movement within Sierra Leone between summer and fall in 2014, and that the current outbreak in Guinea stems from two very distinct genetic sources. It's also possible to scrub through time to see when viral samples appear and to zoom into particular phylogenetic clades by clicking on branches in the tree. Samples can also colored by date of sampling and can be subsetted to particular regions or to particular data sources.
Sequence data for Ebola has been a valuable and scarce resource. Here, Andrew Rambaut has graciously contributed a curated dataset containing 808 viral genomes, collected from publicly available sources, including the European Mobile Lab, the Viral Hemorrhagic Fever Consortium, the China CDC, USAMRIID and the US CDC. However, especially relevant, is the amazing work by Nick Loman, Paul Kellam and Ian Goodfellow providing sequences from April and May 2015 in Guinea and Sierra Leone. We're hopeful that with such timely data and tools to analyze this data and put it into context, we can understand better the current patterns of Ebola transmission and geographic spread, which could aid in surveillance and control efforts. With help from Andrew, Nick, Paul and Ian, we're hoping to keep this updated as new sequences come in.