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. 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. 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. 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. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. Viral infections remain a serious global health issue. 8Center for Infection Medicine and Zoonoses Research, Hannover, Germany.7Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven, Netherlands.6Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.5Conservation Genetics Laboratory, National Institute for Environmental Protection and Research (ISPRA), Bologna, Italy.4Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.3Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.2Viroclinics Biosciences, Rotterdam, Netherlands.1Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands.Smits 1,2 †, Rogier Bodewes 1 †, Aritz Ruiz-Gonzalez 3,4,5, Wolfgang Baumgärtner 6, Marion P.
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