Check out my new review with Dr. Austin L. Hughes discussing simple computational methods for studying the evolution of viruses in their hosts. When studying natural isolates of viruses, or viruses throughout the course of infection experiments, one can determine the potential genomic regions in which positive natural selection works to evade the host’s immune system. This knowledge can help direct vaccine development. We make available SNPGenie, a script-based program for the necessary statistical analyses. Focusing on the example of simian hemorrhagic fever virus (SHFV), we highlight the following:
- Next generation sequencing (NGS) can yield insights into within-host viral evolution.
- Synonymous and nonsynonymous nucleotide diversity can be estimated from NGS data.
- Nucleotide diversity estimates can provide insights into population structure and natural selection.
- The data can illuminate both practical and theoretical issues regarding the evolution of viruses during infection.
Nelson CW, Hughes AL  Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing. Infection, Genetics and Evolution 30:1-7.