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Viruses 2016, 8(3), 60; doi:10.3390/v8030060

From Conventional to Next Generation Sequencing of Epstein-Barr Virus Genomes

Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Author to whom correspondence should be addressed.
Academic Editors: Johnson Mak, Peter Walker and Marcus Thomas Gilbert
Received: 23 December 2015 / Revised: 18 February 2016 / Accepted: 19 February 2016 / Published: 24 February 2016
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Abstract

Genomic sequences of Epstein–Barr virus (EBV) have been of interest because the virus is associated with cancers, such as nasopharyngeal carcinoma, and conditions such as infectious mononucleosis. The progress of whole-genome EBV sequencing has been limited by the inefficiency and cost of the first-generation sequencing technology. With the advancement of next-generation sequencing (NGS) and target enrichment strategies, increasing number of EBV genomes has been published. These genomes were sequenced using different approaches, either with or without EBV DNA enrichment. This review provides an overview of the EBV genomes published to date, and a description of the sequencing technology and bioinformatic analyses employed in generating these sequences. We further explored ways through which the quality of sequencing data can be improved, such as using DNA oligos for capture hybridization, and longer insert size and read length in the sequencing runs. These advances will enable large-scale genomic sequencing of EBV which will facilitate a better understanding of the genetic variations of EBV in different geographic regions and discovery of potentially pathogenic variants in specific diseases. View Full-Text
Keywords: Epstein-Barr virus; Next-generation sequencing; target capture; genome assembly Epstein-Barr virus; Next-generation sequencing; target capture; genome assembly
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Kwok, H.; Chiang, A.K.S. From Conventional to Next Generation Sequencing of Epstein-Barr Virus Genomes. Viruses 2016, 8, 60.

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