We just had a big paper accepted in Nature, which looks at the entirety of the West African Ebola virus epidemic of 2013-2015. The project has existed in a variety of incarnations for well over a year with hints here and there of something big in the making, which unsurprisingly is the last bit of work that followed me from my PhD in Edinburgh to Seattle.
Whereas most publications over the last couple of years have focused on specific regions of the three most affected countries (Sierra Leone, Liberia and Guinea) and over specific time periods, we have analysed all publicly available data (comprising over 5% of all known Ebola virus disease cases!) to arrive at an overarching narrative for the epidemic. By using a Bayesian generalised linear model jointly with phylogenetic inference we not only reconstructed the history of the epidemic from its beginning to its end, but also inferred where the virus had been and what factors were associated with its spread. Our key findings are that:
Ebola virus migration largely followed a classic gravity model with international borders acting as potent barriers. Large population centers tended to receive more infected travellers, especially if incoming cases were from locations that were physically closer. However, migration was reduced if locations were in different countries (i.e. separated by an international border) and further apart.
Regions immediately bordering the three most affected countries, in Guinea-Bissau, Senegal, Mali, and Cote d'Ivoire, were spared their own Ebola outbreaks largely because of their remoteness. By looking into correlates of local Ebola virus proliferation we identified regions of these four neighbouring countries that had the potential to develop large outbreaks, had the virus been introduced.
The population of Ebola virus in West Africa was comprised of small mobile transmission chains, rather than large sweeping outbreaks. Individual transmission chains had poor persistence within any given location, so migration played a key role in sustaining the epidemic.
Beyond science our work exemplifies the slow turnover of ideas that has been taking place in the field. First and foremost, the West African epidemic was the first infectious disease epidemic of its kind, where the sequence data were generated, analysed and shared in real time. It is a huge step in the right direction and could not possibly have happened without the data collectors' efforts, support and trust. I sincerely hope that the collaborative spirit of 2014-2015 lives on for when the next outbreak hits.
Secondly, there is a lot to be said about leveraging cutting edge technologies against challenges like the West African Ebola virus epidemic. I doubt we could have learned nearly as much about this epidemic from small regions of the viral genome (as was convention for sequencing just years before), nor from a small number of of strains. This wouldn't have happened were it not for vast advances in sequencing technology. Now you can pick and choose from any number of sequencing platforms tailored to your needs, be it identifying rare viral variants within individual patients or bringing a sequencer anywhere you go in your pocket.
Lastly, our work is one of many other publications that highlight how important sequencing is to modern infectious disease outbreak response. Sequencing is occasionally equated with stamp collecting, which unjustly ignores the unparalleled perspective that sequence data offer into the heart of any outbreak - the history of the pathogen itself. A handful of sequences go a long way in the right hands, like identifying the origins of the epidemic, documenting unusual patterns of transmission, tracking individual transmission chains in the last stages of the epidemic and linking flare ups of Ebola virus to latent infections, to name a few.
And finally I would like to point out that work of such proportions does not happen in a vacuum. Although there were many who have directly or indirectly contributed to this project, Philippe Lemey, Marc Suchard, Trevor Bedford, Andy Tatem, Luiz Max Carvalho and Andrew Rambaut were the real analytical, theoretical and creative masterminds behind the whole thing. Many thanks for letting me be a part of something this big and exciting.