Challenges in the analysis of viral metagenomes

Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam; Robertson, David L; Prosperi, Mattia

V C The Author 2016. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/ licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact High throughput (or so-called 'next generation') sequencing of viruses during the most recent outbreaks of MERS in South Arabia (Gire et al. 2014; Carroll et al. 2015; Park et al. 2015) and Ebola in West Africa (Quick, J et al. 2016 ) has facilitated rapid identification of transmission chains, rates of viral evolution, and evidence of the zoonotic origin of these outbreaks. Access to such information during initial stages of an outbreak would offer invaluable insight into when, where, and how an epidemic might emerge, informing intervention and mitigation measures or even stopping it altogether. A major step towards this goal is therefore to identify existing zoonotic and environmental pathogens with pandemic potential. This is a significant undertaking, demanding considerable investment and close collaboration between government, NGOs and academia, for example, the USAID program PREDICT http://www.vetmed.ucdavis.edu/ohi/predict/index.cfm, as well as on the ground surveillance by local authorities and scientists in areas of the world most at risk.