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Virus Res. 2017 Jul 15;239:136-142. doi: 10.1016/j.virusres.2017.02.002. Epub 2017 Feb 9.

Origins and challenges of viral dark matter.

Author information

1
Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
2
Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: davewang@wustl.edu.

Abstract

The accurate classification of viral dark matter - metagenomic sequences that originate from viruses but do not align to any reference virus sequences - is one of the major obstacles in comprehensively defining the virome. Depending on the sample, viral dark matter can make up from anywhere between 40 and 90% of sequences. This review focuses on the specific nature of dark matter as it relates to viral sequences. We identify three factors that contribute to the existence of viral dark matter: the divergence and length of virus sequences, the limitations of alignment based classification, and limited representation of viruses in reference sequence databases. We then discuss current methods that have been developed to at least partially circumvent these limitations and thereby reduce the extent of viral dark matter.

KEYWORDS:

Viral dark matter; Viral metagenome; Virome; Virus discovery

PMID:
28192164
DOI:
10.1016/j.virusres.2017.02.002
[Indexed for MEDLINE]

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