title: The full-length DNA sequence of Epstein Barr virus from a human gastric carcinoma cell line, SNU-719.
abstract: The consistent presence of Epstein-Barr virus (EBV) in malignant cells of EBV-associated gastric carcinoma (EBVaGC) suggests it plays an important role during the development of EBVaGC. However, the entire genomic sequence of EBV from EBVaGC has yet to be determined. This study first determined, annotated, and analyzed the full genomic sequence of EBV from the naturally infected gastric carcinoma cell line SNU-719 using next-generation sequencing and comparative analyses. In consistent with the notion that EBV sequence isolates better reflect their geographic area than tissue origin, the SNU-719 EBV (named as GC1) was categorized as an East Asian type I EBV. Compared with the prototype B95.8 sequence, SNU-719 EBV contained 1372 variations, with 937 and 435 within coding and non-coding regions, respectively. Of the 937 variations, 465 were non-synonymous changes, while 472 synonymous changes included partial internal deletions in the coding regions of LMP1 and gp350. The RNAseq transcriptome revealed that multiple BART transcripts comprised the majority of EBV RNA reads. The SNU-719 EBV expressed high levels of BART, LF3, BHLF1, and BNLF2. Evidence of RNA editing at multiple sites in the host chromosome was found; however, no evidence of genome integration was seen. The annotated SNU-719 EBV sequence will be a useful reference in future EBVaGC studies.
authors.affiliation: Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, Korea.|Samsung Biomedical Research Institute (SBRI), Samsung Electronics Co, Ltd., Seoul, Korea.
authors.forename: Kyung-A
authors.initials: KA
authors.lastname: Song
authors.affiliation: Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.
authors.forename: San-Duk
authors.initials: SD
authors.lastname: Yang
authors.affiliation: Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.
authors.forename: Jinha
authors.initials: J
authors.lastname: Hwang
authors.affiliation: Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea. jongil@snu.ac.kr.|Department of Biochemistry, Seoul National University College of Medicine, 103 Daehakno, Jongnogu, Seoul, 110-799, Korea. jongil@snu.ac.kr.|Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Korea. jongil@snu.ac.kr.
authors.forename: Jong-Il
authors.initials: JI
authors.lastname: Kim
authors.affiliation: Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, Korea. mkang@skku.edu.|Samsung Biomedical Research Institute (SBRI), Samsung Electronics Co, Ltd., Seoul, Korea. mkang@skku.edu.
authors.forename: Myung-Soo
authors.initials: MS
authors.lastname: Kang
mesh_terms: D001483:Base Sequence; D002352:Carrier Proteins / Q000096:biosynthesis / Q000235:genetics; D045744:Cell Line, Tumor; D002874:Chromosome Mapping; D019309:Epstein-Barr Virus Nuclear Antigens / Q000235:genetics*; D019143:Evolution, Molecular; D017353:Gene Deletion; D004854:Herpesvirus 4, Human / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D017423:Sequence Analysis, RNA; D000069456:Silent Mutation; D013274:Stomach Neoplasms / Q000821:virology*; D014157:Transcription Factors; D059467:Transcriptome; D014763:Viral Matrix Proteins / Q000096:biosynthesis / Q000235:genetics; D014764:Viral Proteins / Q000096:biosynthesis / Q000235:genetics
chemical_list: C485676:ARL2BP protein, human; C539239:BNLF21 protein, human herpesvirus 4; D002352:Carrier Proteins; C037662:EBV-associated membrane antigen, Epstein-Barr virus; D019309:Epstein-Barr Virus Nuclear Antigens; C473028:LF3 protein, Epstein-Barr virus; D014157:Transcription Factors; D014763:Viral Matrix Proteins; D014764:Viral Proteins
keywords: EBVaGC; Epstein–Barr virus; Gastric carcinoma; Genome; Next-generation sequencing; RNAseq