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.
Highlights
Epstein–Barr virus is a gamma-herpesvirus which infects more than 90% of the world’s population.It is associated with cancers such as Hodgkin’s lymphoma, Burkitt’s lymphoma, gastric cancer, nasopharyngeal carcinoma, and other conditions, such as post-transplant lymphoproliferative diseases and infectious mononucleosis
More than 1400 point mutations were identified by comparing against the type 1 reference, some of which were found in high frequency in NPC biopsies of the same geographical region, suggesting that GD1 is representative of the Epstein–Barr virus (EBV) strains found in Southern Chinese NPC patients
The sequencing of EBV strains in Akata and Mutu cell line was made feasible by taking advantage of the properties of lytic replication of EBV in these lines to increase the viral copy number
Summary
Epstein–Barr virus is a gamma-herpesvirus which infects more than 90% of the world’s population. It is associated with cancers such as Hodgkin’s lymphoma, Burkitt’s lymphoma, gastric cancer, nasopharyngeal carcinoma, and other conditions, such as post-transplant lymphoproliferative diseases and infectious mononucleosis. South Asia, and Northern Africa [1,2,3,4,5,6] These early studies have only been focused on the individual viral genes. Very few studies have been carried out to investigate how genetic variations of EBV on a whole-genome scale might influence infection or pathogenesis of EBV-associated diseases. This review provides an overview of how the sequences of published EBV genomes have been determined, and the bioinformatics analyses involved
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