Challenges and opportunities: A framework for analysis of metagenomic sequencing data

Abstract

Background: Next-generation sequencing (NGS) allows the analysis of viral sequence variants from select natural environments, presenting a novel opportunity for understanding the genetic diversity present in these ecosystems, virus evolution and allows outbreaks to be followed in great detail.

Objective: To gain a better understanding of the potential factors influencing the spread of viruses (in space and time) in small farm ecosystems, we are currently investigating how these viral species are evolving across their entire geographical distribution using a combination of Genomics and Bioinformatics approaches.

Methodology: We have developed a bioinformatics pipeline for automating the analyses of viral metagenomes. Furthermore, we are currently developing an information (GISbased) system for collecting, analyzing and reporting of all viral data related to small farm ecosystems to supplement the computational pipeline. Application of these methodologies to viruses will make it possible to explore viral diversity through automatically constructed time-measured phylogenies and perform comparison against thier viromes.

Results: This bioinformatics pipeline is designed to provide answers to questions such as when and where did an epidemic begin, how viral populations are genetically structured in space and what are the key determinants of viral spread between geographical regions? The answers to these questions provide insights into the potential factors underlying both the spatio-temporal dynamics and evolution of members of viral families and will help to inform governmental policy aimed at restricting the movements of diseased plant and animal materials and virus-carrying insects within and across national borders by identifying both key transmission routes and the locations in Africa where viruses with increased disease-causing potential commonly arise.