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Review
. 2015 Oct 1:6:1069.
doi: 10.3389/fmicb.2015.01069. eCollection 2015.

Recovering full-length viral genomes from metagenomes

Saskia L Smits  1 , Rogier Bodewes  1 , Aritz Ruiz-González  2 , Wolfgang Baumgärtner  3 , Marion P Koopmans  4 , Albert D M E Osterhaus  5 , Anita C Schürch  1
Affiliations
Review

Recovering full-length viral genomes from metagenomes

Saskia L Smits et al. Front Microbiol. .

Abstract

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: assembly; coverage analysis; k-mer analysis; metagenomics; motif discovery; virus discovery; viruses; zoonotic pathogens.

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Figures

Figure 1
Figure 1
Metagenome composition before and after genome finishing. Red bars: Percentage of reads of the metagenome assigned to target genome after similarity searches and before genome finishing. Blue bars: Percentage of reads of the metagenome assigned to target genome after genome finishing strategies were applied to the target genome. DRV, dolphin rhabdovirus; RFFRV, red fox fecal rhabdovirus; PNV, python nidovirus.
Figure 2
Figure 2
Genome completeness before and after genome finishing. (A) Genome of dolphin rhabdovirus (DRV). (B) Genome of red fox fecal rhabdovirus (RFFRV). (C) Genome of python nidovirus (PNV). Indicated is contig size after initial genome assembly (red) and after genome finishing (blue). Striped line at the 5′ end of PNV indicates putative unresolved 5′ end.
Figure 3
Figure 3
Steps in recovery of full-length viral genomes from metagenomes. For description see article text.
See this image and copyright information in PMC

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