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Viruses 2011, 3(10), 1849-1869; doi:10.3390/v3101849

Next Generation Sequencing Technologies for Insect Virus Discovery

Department of Entomology, Iowa State University, Ames, IA 50011, USA
* Author to whom correspondence should be addressed.
Received: 2 September 2011 / Revised: 15 September 2011 / Accepted: 19 September 2011 / Published: 10 October 2011
(This article belongs to the Special Issue Insect Viruses)
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Insects are commonly infected with multiple viruses including those that cause sublethal, asymptomatic, and latent infections. Traditional methods for virus isolation typically lack the sensitivity required for detection of such viruses that are present at low abundance. In this respect, next generation sequencing technologies have revolutionized methods for the discovery and identification of new viruses from insects. Here we review both traditional and modern methods for virus discovery, and outline analysis of transcriptome and small RNA data for identification of viral sequences. We will introduce methods for de novo assembly of viral sequences, identification of potential viral sequences from BLAST data, and bioinformatics for generating full-length or near full-length viral genome sequences. We will also discuss implications of the ubiquity of viruses in insects and in insect cell lines. All of the methods described in this article can also apply to the discovery of viruses in other organisms.
Keywords: insect virus; next generation sequencing; virus discovery; small RNA; transcriptome insect virus; next generation sequencing; virus discovery; small RNA; transcriptome
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Liu, S.; Vijayendran, D.; Bonning, B.C. Next Generation Sequencing Technologies for Insect Virus Discovery. Viruses 2011, 3, 1849-1869.

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