A real-time, portable genome sequencing system was developed to enable rapid genomic surveillance of the Ebola virus during the 2014-2015 West African epidemic. The system, based on the MinION nanopore sequencer, allowed for the generation of genome sequences in under 24 hours after receiving a positive sample, with sequencing taking as little as 15-60 minutes. This enabled the identification of distinct sub-lineages of the Ebola virus, which is critical for outbreak monitoring and control. The system was transported to Guinea and used to sequence 142 Ebola virus samples collected between March and October 2015. The results showed that real-time genomic surveillance is feasible in resource-limited settings and can be rapidly established to monitor outbreaks. The MinION sequencer is highly portable, weighing less than 100 grams, and can be powered via a USB port from a laptop. It uses a nanopore to measure electrical current changes as DNA passes through, enabling the sequencing of long DNA molecules. However, it has a higher error rate compared to high-throughput sequencers. To improve accuracy, the system used targeted reverse transcriptase PCR to isolate sufficient DNA for sequencing. A panel of 38 primer pairs was designed to span the EBOV genome, allowing for the sequencing of 142 samples. The system was deployed in Guinea and used to generate real-time genomic data, which was shared with national and international health organizations. The data was used to track the evolution of the virus and identify transmission patterns between Guinea and Sierra Leone. The study also highlighted the challenges of conducting genomic surveillance in resource-limited settings, including the lack of reliable power and internet connectivity. Despite these challenges, the system proved effective in providing real-time genomic data for outbreak response. The study demonstrated the potential of portable genome sequencing for rapid genomic surveillance during outbreaks. It showed that real-time genomic data can be used to inform public health decisions and improve the understanding of viral evolution. The results also highlighted the importance of data sharing and collaboration in outbreak response. The study was part of a larger project funded by the European Union's Horizon 2020 program and involved multiple institutions and organizations. The findings have important implications for the management of future outbreaks and the development of genomic surveillance systems in resource-limited settings.A real-time, portable genome sequencing system was developed to enable rapid genomic surveillance of the Ebola virus during the 2014-2015 West African epidemic. The system, based on the MinION nanopore sequencer, allowed for the generation of genome sequences in under 24 hours after receiving a positive sample, with sequencing taking as little as 15-60 minutes. This enabled the identification of distinct sub-lineages of the Ebola virus, which is critical for outbreak monitoring and control. The system was transported to Guinea and used to sequence 142 Ebola virus samples collected between March and October 2015. The results showed that real-time genomic surveillance is feasible in resource-limited settings and can be rapidly established to monitor outbreaks. The MinION sequencer is highly portable, weighing less than 100 grams, and can be powered via a USB port from a laptop. It uses a nanopore to measure electrical current changes as DNA passes through, enabling the sequencing of long DNA molecules. However, it has a higher error rate compared to high-throughput sequencers. To improve accuracy, the system used targeted reverse transcriptase PCR to isolate sufficient DNA for sequencing. A panel of 38 primer pairs was designed to span the EBOV genome, allowing for the sequencing of 142 samples. The system was deployed in Guinea and used to generate real-time genomic data, which was shared with national and international health organizations. The data was used to track the evolution of the virus and identify transmission patterns between Guinea and Sierra Leone. The study also highlighted the challenges of conducting genomic surveillance in resource-limited settings, including the lack of reliable power and internet connectivity. Despite these challenges, the system proved effective in providing real-time genomic data for outbreak response. The study demonstrated the potential of portable genome sequencing for rapid genomic surveillance during outbreaks. It showed that real-time genomic data can be used to inform public health decisions and improve the understanding of viral evolution. The results also highlighted the importance of data sharing and collaboration in outbreak response. The study was part of a larger project funded by the European Union's Horizon 2020 program and involved multiple institutions and organizations. The findings have important implications for the management of future outbreaks and the development of genomic surveillance systems in resource-limited settings.