Cultivation of newly identified viruses to retrieve their genomic sequences is often difficult. Often, metagenomic approaches are used to identify complete viral genomes from sequence and for phylogenetic characterization of these new viruses. The de novo assembly of 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.

Selected references

Assembly of viral genomes from metagenomes Saskia L Smits, Rogier Bodewes, Aritz Ruiz-Gonzalez, Wolfgang Baumgärtner, Marion P Koopmans, Albert DME Osterhaus, Anita C Schürch Frontiers in microbiology 5, 714

Exploring the potential of next-generation sequencing in detection of respiratory viruses Slinporn Prachayangprecha, Claudia ME Schapendonk, Marion P Koopmans, Albert DME Osterhaus, Anita C Schürch, Suzan D Pas, Annemiek A van der Eijk, Yong Poovorawan, Bart L Haagmans, Saskia L Smits Journal of clinical microbiology 52 (10), 3722-3730

Recovering full-length viral genomes from metagenomes Saskia L Smits, Rogier Bodewes, Aritz Ruiz-González, Wolfgang Baumgärtner, Marion P Koopmans, Albert DME Osterhaus, Anita C Schürch Frontiers in microbiology 6, 1069