Recovering full-length viral genomes from metagenomes

Frontiers in Microbiology

Albertus DME eOsterhaus¹  Saskia eSmits²  Rogier eBodewes³  Aritz eRuiz-Gonzalez⁵  Marion eKoopmans⁶  Anita C. Schürch⁷  Wolfgang eBaumgärtner⁸ 

[1] Center for Infection Medicine and Zoonoses Research;Erasmus Medical Centre;Faculty of Veterinary Medicine, Utrecht University;Lascaray Research Center, University of the Basque Country (UPV/EHU);National Institute for Environmental Protection and Research (ISPRA);National Institute for Public Health and the Environment;University Medical Center Utrecht;University of Veterinary Medicine Hannover;University of the Basque Country (UPV/EHU);

关键词: Metagenomics;    Viruses;    Assembly;    motif discovery;    zoonotic pathogens;    virus discovery;   

DOI  :  10.3389/fmicb.2015.01069

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown