Frontiers in Microbiology (Oct 2015)

Recovering full-length viral genomes from metagenomes

  • Saskia eSmits,
  • Rogier eBodewes,
  • Rogier eBodewes,
  • Aritz eRuiz-Gonzalez,
  • Aritz eRuiz-Gonzalez,
  • Aritz eRuiz-Gonzalez,
  • Wolfgang eBaumgärtner,
  • Marion eKoopmans,
  • Marion eKoopmans,
  • Albertus DME eOsterhaus,
  • Albertus DME eOsterhaus,
  • Anita C. Schürch,
  • Anita C. Schürch

DOI
https://doi.org/10.3389/fmicb.2015.01069
Journal volume & issue
Vol. 6

Abstract

Read online

Infectious disease metagenomics is driven by the question: what is causing the disease? in contrast to classical metagenome studies which are guided by what is out there?. In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.

Keywords