title: Assembly of viral genomes from metagenomes.
abstract: Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.
authors.affiliation: Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Viroclinics Biosciences Rotterdam, Netherlands.
authors.forename: Saskia L
authors.initials: SL
authors.lastname: Smits
authors.affiliation: Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands.
authors.forename: Rogier
authors.initials: R
authors.lastname: Bodewes
authors.affiliation: Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Conservation Genetics Laboratory, National Institute for Environmental Protection and Research (ISPRA) Bologna, Italy.
authors.forename: Aritz
authors.initials: A
authors.lastname: Ruiz-Gonzalez
authors.affiliation: Department of Pathology, University of Veterinary Medicine Hannover Hannover, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Baumgärtner
authors.affiliation: Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment Bilthoven, Netherlands.
authors.forename: Marion P
authors.initials: MP
authors.lastname: Koopmans
authors.affiliation: Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Viroclinics Biosciences Rotterdam, Netherlands ; Center for Infection Medicine and Zoonoses Research Hannover, Germany.
authors.forename: Albert D M E
authors.initials: AD
authors.lastname: Osterhaus
authors.affiliation: Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands.
authors.forename: Anita C
authors.initials: AC
authors.lastname: Schürch
keywords: assembly; metagenome; pathogen; viral metagenomics; virome; virus; virus discovery