Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology

Haiyan Lei,Shyh-Ching Lo,Bingjie Li,Guo-Chiuan Hung,Tianwei Li,Shien Tsai

doi:10.1186/1471-2164-14-804

Haiyan Lei, Shyh-Ching Lo + Show 4 more

Open Access

https://doi.org/10.1186/1471-2164-14-804

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Journal: BMC Genomics	Publication Date: Nov 19, 2013
Citations: 34	License type: cc-by

Affiliation: Center for Biologics Evaluation and Research

Abstract

BackgroundWe conducted genomic sequencing to identify Epstein Barr Virus (EBV) genomes in 2 human peripheral blood B lymphocytes that underwent spontaneous immortalization promoted by mycoplasma infections in culture, using the high-throughput sequencing (HTS) Illumina MiSeq platform. The purpose of this study was to examine if rapid detection and characterization of a viral agent could be effectively achieved by HTS using a platform that has become readily available in general biology laboratories.ResultsRaw read sequences, averaging 175 bps in length, were mapped with DNA databases of human, bacteria, fungi and virus genomes using the CLC Genomics Workbench bioinformatics tool. Overall 37,757 out of 49,520,834 total reads in one lymphocyte line (# K4413-Mi) and 28,178 out of 45,335,960 reads in the other lymphocyte line (# K4123-Mi) were identified as EBV sequences. The two EBV genomes with estimated 35.22-fold and 31.06-fold sequence coverage respectively, designated K4413-Mi EBV and K4123-Mi EBV (GenBank accession number KC440852 and KC440851 respectively), are characteristic of type-1 EBV.ConclusionsSequence comparison and phylogenetic analysis among K4413-Mi EBV, K4123-Mi EBV and the EBV genomes previously reported to GenBank as well as the NA12878 EBV genome assembled from database of the 1000 Genome Project showed that these 2 EBVs are most closely related to B95-8, an EBV previously isolated from a patient with infectious mononucleosis and WT-EBV. They are less similar to EBVs associated with nasopharyngeal carcinoma (NPC) from Hong Kong and China as well as the Akata strain of a case of Burkitt’s lymphoma from Japan. They are most different from type 2 EBV found in Western African Burkitt’s lymphoma.

Highlights

We conducted genomic sequencing to identify Epstein Barr Virus (EBV) genomes in 2 human peripheral blood B lymphocytes that underwent spontaneous immortalization promoted by mycoplasma infections in culture, using the high-throughput sequencing (HTS) Illumina MiSeq platform
We identified and extracted EBV sequences from genomic sequencing data of the 2 B-lymphocyte cell lines, assembled them into single genomes and compared them with the sequences of all the EBV genomes previously reported to the GenBank
We used the Illumina MiSeq sequencing platform, a next generation sequencing (NGS) technology and convenient computational tools, CLC Genomics Workbench, to identify and extract EBV sequences from human B lymphocyte cell lines that underwent spontaneous immortalization promoted by infection of mycoplasma in culture

Summary

Introduction

We conducted genomic sequencing to identify Epstein Barr Virus (EBV) genomes in 2 human peripheral blood B lymphocytes that underwent spontaneous immortalization promoted by mycoplasma infections in culture, using the high-throughput sequencing (HTS) Illumina MiSeq platform. B95-8 (GenBank accession number V01555.2), derived from a North American case of infectious mononucleosis [9], was the first completely sequenced EBV genome. AG876 (DQ279927.1) from a Western African case of Burkitt’s lymphoma is the only complete type 2 EBV sequence to date [12]; GD1 (AY961628.3), GD2 (HQ020558.1) and HKNPC1 (JQ009376.1) are all EBV genomes derived from NPC patients or NPC tumours. 2 EBV genomes, Akata (KC207813) and Mutu (KC207814), were reported recently from cases of Burkitt’s lymphomas from Japan and Kenya, respectively, by NGS technology [16]

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