Zaire ebolavirus Raw sequence reads

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new outbreaks going forward, rapid epidemiological tracing of cases and contacts is required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provides a powerful tool for public health epidemic control efforts. By full virus genome sequencing in as little as 24 hours at the Mateneh Ebola Treatment Centre, we produced 554 EBOV genomes from EVD cases across Sierra Leone, up to September 15th 2015. This enabled phylogenetic tracking of all new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing, but also identify obscure transmission chains involving semen and breast milk body fluids. Further, we evaluate the contribution of persistent infection to the epidemic and conservatively estimate that the majority of onward transmission occurs within a week after infection. The coupling of viral phylogenetic methods with infection control management should therefore form a major part of outbreak emergency responses