Advances in the application of high-throughput sequencing in invertebrate virology

[Display omitted] •Advances in high-throughput sequencing methods have revolutionised virology research.•Whole Genome Sequencing facilitates discovery and characterization of viral genomes.•RNA-Seq has great utility for studying host-pathogen interactions during infection.•Metagenomic methods enable...

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Bibliographic Details
Published in:Journal of invertebrate pathology 2017-07, Vol.147, p.145-156
Main Authors: van Aerle, R., Santos, E.M.
Format: Article
Language:English
Subjects:
Animals
Bioinformatics
Computational Biology - methods
Computational Biology - trends
Genome, Viral
High-Throughput Nucleotide Sequencing - trends
Host-pathogen interactions
Host-Pathogen Interactions - genetics
Invertebrates - virology
Metagenomics
Next-generation sequencing
RNA-Seq
Viruses - classification
Viruses - genetics
Viruses - isolation & purification
Whole genome assembly
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Summary:[Display omitted] •Advances in high-throughput sequencing methods have revolutionised virology research.•Whole Genome Sequencing facilitates discovery and characterization of viral genomes.•RNA-Seq has great utility for studying host-pathogen interactions during infection.•Metagenomic methods enable studies on diversity and composition of viral communities.•Good hypothesis and experimental design are essential for the success of the study. Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.
ISSN:0022-2011
1096-0805
DOI:10.1016/j.jip.2017.02.006