title: Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology.
abstract: Epstein-Barr virus (EBV)-encoded molecules have been detected in the tumor tissues of several cancers, including nasopharyngeal carcinoma (NPC), suggesting that EBV plays an important role in tumorigenesis. However, the nature of EBV with respect to genome width in vivo and whether EBV undergoes clonal expansion in the tumor tissues are still poorly understood. In this study, next-generation sequencing (NGS) was used to sequence DNA extracted directly from the tumor tissue of a patient with NPC. Apart from the human sequences, a clinically isolated EBV genome 164.7 kb in size was successfully assembled and named GD2 (GenBank accession number HQ020558). Sequence and phylogenetic analyses showed that GD2 was closely related to GD1, a previously assembled variant derived from a patient with NPC. GD2 contains the most prevalent EBV variants reported in Cantonese patients with NPC, suggesting that it might be the prevalent strain in this population. Furthermore, GD2 could be grouped into a single subtype according to common classification criteria and contains only 6 heterozygous point mutations, suggesting the monoclonal expansion of GD2 in NPC. This study represents the first genome-wide analysis of a clinical isolate of EBV directly extracted from NPC tissue. Our study reveals that NGS allows the characterization of genome-wide variations of EBV in clinical tumors and provides evidence of monoclonal expansion of EBV in vivo. The pipeline could also be applied to the study of other pathogen-related malignancies. With additional NGS studies of NPC, it might be possible to uncover the potential causative EBV variant involved in NPC.
authors: State Key Laboratory of Oncology in Southern China, Department of Experimental Research, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou 510060, China.
authors: Pan
authors: P
authors: Liu
authors: Xiaodong
authors: X
authors: Fang
authors: Zizhen
authors: Z
authors: Feng
authors: Yun-Miao
authors: YM
authors: Guo
authors: Rou-Jun
authors: RJ
authors: Peng
authors: Tengfei
authors: T
authors: Liu
authors: Zhiyong
authors: Z
authors: Huang
authors: Yue
authors: Y
authors: Feng
authors: Xiaoqing
authors: X
authors: Sun
authors: Zhiqiang
authors: Z
authors: Xiong
authors: Xiaosen
authors: X
authors: Guo
authors: Sha-Sha
authors: SS
authors: Pang
authors: Bo
authors: B
authors: Wang
authors: Xiaojuan
authors: X
authors: Lv
authors: Fu-Tuo
authors: FT
authors: Feng
authors: Da-Jiang
authors: DJ
authors: Li
authors: Li-Zhen
authors: LZ
authors: Chen
authors: Qi-Sheng
authors: QS
authors: Feng
authors: Wen-Lin
authors: WL
authors: Huang
authors: Mu-Sheng
authors: MS
authors: Zeng
authors: Jin-Xin
authors: JX
authors: Bei
authors: Yong
authors: Y
authors: Zhang
authors: Yi-Xin
authors: YX
authors: Zeng
mesh_terms: D002277:Carcinoma; D002681:China; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics*; D020031:Epstein-Barr Virus Infections / Q000150:complications*; D004854:Herpesvirus 4, Human / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000821:virology*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D004279:DNA, Viral