EBV基因组测序的研究进展
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摘要
EB病毒在全世界范围内广泛分布,科学家们发现EB病毒与人类单核细胞增多症及多种恶性肿瘤相关。EB病毒的地理分布和EB病毒相关疾病的地方病发病率特点促使人们研究是否有不同的EB病毒株参与疾病的发展。第一代测序技术的低效率和高成本限制了全基因组EBV的测序,随着第二代测序技术(NGS)的发展,越来越多的EB病毒基因组序列发表。这将有助于更好地理解EBV在不同地理区域的遗传变异,并在特定疾病中发现可能的致病变异。本文概述了已发表的EBV基因组的概况及用于生成这些序列的测序技术和生物信息学分析,探讨EBV全基因组未来的研究方向。
Epstein-Barr virus(EBV) is widely distributed all over the world. Scientists have found that EBV is associated with infectious mononucleosis and various malignant tumors. Certain EBV-associated diseases, such as Burkitt lymphomas and nasopharyngeal carcinomas, are endemic and exhibit skewed geographic distribution worldwide. The geographical distribution of EBV strains and the incidence of EBV-associated diseases have prompted studies of whether distinct strains of EBV are involved. Sequencing of EBV has been limited by the inefficiency and cost of first-generation sequencing technology. Recent advances in sequencing technology have enabled high-throughput sequencing of the EBV genome. With the development of next-generation sequencing(NGS), a number of EBV genomes have been published. These genomes were sequenced using different approaches such as enrichment of EBV DNA or no enrichment. This review provides an overview of the EBV genomes published and a description of the sequencing technology and bioinformatic analyses used to examine EBV sequences. This review also describes recent advances and potential future directions for EBV sequencing.
Epstein-Barr virus(EBV) is widely distributed all over the world. Scientists have found that EBV is associated with infectious mononucleosis and various malignant tumors. Certain EBV-associated diseases, such as Burkitt lymphomas and nasopharyngeal carcinomas, are endemic and exhibit skewed geographic distribution worldwide. The geographical distribution of EBV strains and the incidence of EBV-associated diseases have prompted studies of whether distinct strains of EBV are involved. Sequencing of EBV has been limited by the inefficiency and cost of first-generation sequencing technology. Recent advances in sequencing technology have enabled high-throughput sequencing of the EBV genome. With the development of next-generation sequencing(NGS), a number of EBV genomes have been published. These genomes were sequenced using different approaches such as enrichment of EBV DNA or no enrichment. This review provides an overview of the EBV genomes published and a description of the sequencing technology and bioinformatic analyses used to examine EBV sequences. This review also describes recent advances and potential future directions for EBV sequencing.
引文
[1] Elgui De Oliveira D,Muller-Coan BG,JSP.Viral carcinogenesis beyond malignant transformation:EBV in the progression of human cancers[J].Trends Microbiol,2016,24(8):649-64.
[2] de Martel C,Ferlay J,Franceschi S,et al.Global burden of cancers attributable to infections in 2008:a review and synthetic analysis[J].Lancet Oncol,2012,13(6):607-15.
[3] Chang ET,Adami HO.The enigmatic epidemiology of nasopharyngeal carcinoma[J].Cancer Epidemiol Biomarkers Prev,2006,15(10):1765-77.
[4] Kelly GL,AB R.Pediatric hematologic malignancies:Non-hodgkin lymphoma[J].Hematology,2007:277-84.
[5] Camargo MC,Murphy G,Koriyama C,et al.Determinants of Epstein-Barr virus-positive gastric cancer:an international pooled analysis[J].Br J Cancer,2011,105(1):38-43.
[6] Young LS,Yao QY,CM R.New type B isolates of Epstein-Barr Virus from Burkitt's lymphoma and from normal individuals in endemic areas[J].J Gen Virol,1987,68(Pt 11):2853-62.
[7] Tzellos S,Farrell P.Epstein-barr virus sequence variation-biology and disease[J].Pathogens,2012,1(2):156-74.
[8] Enrberg DNI,Tran-Thi PPPC,Hu L.Epstein-barr virus genetic variation in vietnamese patients with nasopharyngeal carcinoma:full-length analysis of LMP1[J].Virus Genes,2008,37(2):273-81.
[9] Bonnet M.Amino-acid change in the Epstein-Barr-virus ZEBRA protein in undifferentiated nasopharyngeal carcinomas from Europe and North Africa[J].Int J Cancer,1998,75(4):497-503.
[10] Chang K,Hao S,Lin S,et al.The 30-bp deletion of Epstein-barr virus latent membrane protein-1 gene has no effect in Nasopharyngeal Carcinoma[J].Laryngoscope,2006,116(4):541-6.
[11] Bankier AT,MD B.DNA sequence and expression of the B95-8 Epstein-Barr virus genome[J].Nature,1984,310(5974):207-11.
[12] 徐伟文,邵向阳,徐伟文.下一代测序(NGS)技术的发展及在肿瘤研究的应用[J].分子诊断与治疗杂志,2016,8(05):289-96.
[13] 毛亚文,陈江华.DNA测序技术的发展进程[J].亚热带植物科学,2018,47(01):94-100.
[14] Skare J,Edson C,Farley J,et al.The B95-8 isolate of Epstein-Barr virus arose from an isolate with a standard genome[J].J Virol,1982,44(3):1088-91.
[15] Hummel M.Epstein-Barr virus RNA.VIII.Viral RNA in permissively infected B95-8 cells[J].J Virol,1982,43(1):262-72.
[16] de Jesus O,Smith PR,LC S,et al.Updated Epstein-Barr virus (EBV) DNA sequence and analysis of a promoter for the BART (CST,BARF0) RNAs of EBV[J].J Gen Virol,2003,84(6):1443-50.
[17] Pizzo PA,Magrath IT,Chattopadhyay SK,et al.A new tumour-derived transforming strain of Epstein-Barr virus[J].Nature,1978,272(5654):629-31.
[18] Dolan A,Addison C,Gatherer D,et al.The genome of Epstein-Barr virus type 2 strain AG876[J].Virology,2006,350(1):164-70.
[19] Zeng MS,Li DJ,Liu QL,et al.Genomic sequence analysis of epstein-barr virus strain GD1 from a nasopharyngeal carcinoma patient[J].J Virol,2005,79(24):15323-30.
[20] Liu P,Fang X,Guo YM,et al.Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology[J].J Virol,2011,85(21):11291-9.
[21] Cheung ST,Huang DP,Hui AB,et al.Nasopharyngeal carcinoma cell line (C666-1) consistently harbouring Epstein-Barr virus.[J].Int J Cancer,1999,83(1):121-6.
[22] Tso KK,Yip KY,Mak CK,et al.Complete genomic sequence of Epstein-Barr virus in nasopharyngeal carcinoma cell line C666-1[J].Infect Agent Cancer,2013,8(1):29.
[23] Lin Z,Wang X,Strong MJ,et al.Whole-genome sequencing of the akata and mutu epstein-barr virus strains[J].J Virol,2012,87(2):1172-82.
[24] Tong AH,Lin CH.Genomic sequencing and comparative analysis of Epstein-barr virus genome isolated from primary nasopharyngeal carcinoma biopsy[J].PLoS One,2012,7(5):e36939.
[25] Simbiri KO,Smith NA,Otieno R,et al.Epstein-barr virus genetic variation in lymphoblastoid cell lines derived from kenyan pediatric population[J].PLoS One,2015,10(5):e0125420.
[26] Tsai MH,Raykova A,Klinke O,et al.Spontaneous lytic replication and epitheliotropism define an Epstein-barr virus strain found in carcinomas[J].Cell Rep,2013,5(2):458-70.
[27] Delecluse HJ,Hilsendegen T,Pich D,et al.Propagation and recovery of intact,infectious Epstein-Barr virus from prokaryotic to human cells[J].Proc Natl Acad Sci USA,1998,95(14):8245-50.
[28] 喻正源.全基因组测序与病毒捕获测序技术探讨EB病毒进化及整合规律的初步研究[J].博士,2013.
[29] 张鑫,李敏,张学军.全基因组外显子测序及其应用[J].HEREDITAS (Beijing),2011,8(33):847-56.
[30] Kwok H,Wu CW,Palser AL,et al.Genomic diversity of Epstein-barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples[J].J Virol,2014,88(18):10662-72.
[31] Palser AL,Grayson NE,White RE,et al.Genome diversity of Epstein-barr virus from multiple tumor types and normal infection[J].J Virol,2015,89(10):5222-37.
[32] Kwok H,Chiang A.From Conventional to next generation sequencing of Epstein-barr virus genomes[J].Viruses,2016,8(3):60.
[33] 郑钢.基于下一代测序的短序列匹配与支架算法研究[D].信阳师范学院,2015.
[34] Li H,Durbin R.Fast and accurate short read alignment with Burrows-Wheeler transform[J].Bioinformatics,2009,25(14):1754-60.
[35] Langmead B,Trapnell C,Pop M,et al.Ultrafast and memory-efficient alignment of short DNA sequences to the human genome[J].Genome Biol,2009,10(3):R25.
[36] Li R,Yu C,Li Y,et al.SOAP2:an improved ultrafast tool for short read alignment[J].Bioinformatics,2009,25(15):1966-7.
[37] Huang Q,Petros AM,Virgin HW,et al.Solution structure of the BHRF1 protein from Epstein-barr virus,a homolog of human Bcl-2[J].J Mol Biol,2003,332(5):1123-30.
[38] Stewart JP.The interleukin-10 homolog encoded by Epstein-barr virus-specific cytotoxic T cell and HLA-unrestricted virus enhances the reactivation killer cell responses[J].Virology,1992,191(2):773-82.
[39] 郑广勇,杨桢,曹瑞芳,等.宏基因组大数据分析的质量控制流程规范[J].大数据,2018,4(03):3-12.
[40] Ewing B,Hillier L,Wendl MC,et al.Base-calling of automated sequencer traces usingphred.I[J].Genome Res,1998,8(3):175-85.
[41] Wingett SW.FastQ Screen:A tool for multi-genome mapping and quality control[J].F1000Res,2018(7):1338.
[42] 袁易,王铭杰,张欣欣.第三代测序技术的主要特点及其在病毒基因组研究中的应用[J].微生物与感染,2016,11(06):380-4.
[43] Lei H,Li T,Hung G,et al.Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology[J].BMC genomics,2013,14(1):804.
[44] Song K,Yang S,Hwang J,et al.The full-length DNA sequence of Epstein barr virus from a human gastric carcinoma cell line,SNU-719[J].Virus Genes,2015,51(3):329-37.
[45] Santpere G,Darre F,Blanco S,et al.Genome-wide analysis of wild-type Epstein-barr virus genomes derived from healthy individuals of the 1000 genomes project[J].Genome Biol Evol,2014,6(4):846-60.
[46] Lei H,Li T,Li B,et al.Epstein-barr virus from burkitt lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations[J].Sci Rep,2015,5:16706.
[47] Simbiri KO,Smith NA,Otieno R,et al.Epstein-barr virus genetic variation in lymphoblastoid cell lines derived from kenyan pediatric population[J].PLoS One,10(5):e0125420.
[48] Liu Y,Yang W,Pan Y,et al.Genome-wide analysis of Epstein-barr virus (EBV) isolated from EBV-associated gastric carcinoma (EBVaGC)[J].Oncotarget,2016,7(4):4903-14.
[49] Tu C,Zeng Z,Qi P,et al.Genome-wide analysis of 18 Epstein-barr viruses isolated from primary nasopharyngeal carcinoma biopsy specimens[J].J Virol,2017,91(17):e00301-17.
[50] Wang S,Xiong H,Yan S,et al.Identification and characterization of Epstein-barr virus genomes in lung carcinoma biopsy samples by next-generation sequencing technology[J].Sci Rep,2016,6:26156.
[2] de Martel C,Ferlay J,Franceschi S,et al.Global burden of cancers attributable to infections in 2008:a review and synthetic analysis[J].Lancet Oncol,2012,13(6):607-15.
[3] Chang ET,Adami HO.The enigmatic epidemiology of nasopharyngeal carcinoma[J].Cancer Epidemiol Biomarkers Prev,2006,15(10):1765-77.
[4] Kelly GL,AB R.Pediatric hematologic malignancies:Non-hodgkin lymphoma[J].Hematology,2007:277-84.
[5] Camargo MC,Murphy G,Koriyama C,et al.Determinants of Epstein-Barr virus-positive gastric cancer:an international pooled analysis[J].Br J Cancer,2011,105(1):38-43.
[6] Young LS,Yao QY,CM R.New type B isolates of Epstein-Barr Virus from Burkitt's lymphoma and from normal individuals in endemic areas[J].J Gen Virol,1987,68(Pt 11):2853-62.
[7] Tzellos S,Farrell P.Epstein-barr virus sequence variation-biology and disease[J].Pathogens,2012,1(2):156-74.
[8] Enrberg DNI,Tran-Thi PPPC,Hu L.Epstein-barr virus genetic variation in vietnamese patients with nasopharyngeal carcinoma:full-length analysis of LMP1[J].Virus Genes,2008,37(2):273-81.
[9] Bonnet M.Amino-acid change in the Epstein-Barr-virus ZEBRA protein in undifferentiated nasopharyngeal carcinomas from Europe and North Africa[J].Int J Cancer,1998,75(4):497-503.
[10] Chang K,Hao S,Lin S,et al.The 30-bp deletion of Epstein-barr virus latent membrane protein-1 gene has no effect in Nasopharyngeal Carcinoma[J].Laryngoscope,2006,116(4):541-6.
[11] Bankier AT,MD B.DNA sequence and expression of the B95-8 Epstein-Barr virus genome[J].Nature,1984,310(5974):207-11.
[12] 徐伟文,邵向阳,徐伟文.下一代测序(NGS)技术的发展及在肿瘤研究的应用[J].分子诊断与治疗杂志,2016,8(05):289-96.
[13] 毛亚文,陈江华.DNA测序技术的发展进程[J].亚热带植物科学,2018,47(01):94-100.
[14] Skare J,Edson C,Farley J,et al.The B95-8 isolate of Epstein-Barr virus arose from an isolate with a standard genome[J].J Virol,1982,44(3):1088-91.
[15] Hummel M.Epstein-Barr virus RNA.VIII.Viral RNA in permissively infected B95-8 cells[J].J Virol,1982,43(1):262-72.
[16] de Jesus O,Smith PR,LC S,et al.Updated Epstein-Barr virus (EBV) DNA sequence and analysis of a promoter for the BART (CST,BARF0) RNAs of EBV[J].J Gen Virol,2003,84(6):1443-50.
[17] Pizzo PA,Magrath IT,Chattopadhyay SK,et al.A new tumour-derived transforming strain of Epstein-Barr virus[J].Nature,1978,272(5654):629-31.
[18] Dolan A,Addison C,Gatherer D,et al.The genome of Epstein-Barr virus type 2 strain AG876[J].Virology,2006,350(1):164-70.
[19] Zeng MS,Li DJ,Liu QL,et al.Genomic sequence analysis of epstein-barr virus strain GD1 from a nasopharyngeal carcinoma patient[J].J Virol,2005,79(24):15323-30.
[20] Liu P,Fang X,Guo YM,et al.Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology[J].J Virol,2011,85(21):11291-9.
[21] Cheung ST,Huang DP,Hui AB,et al.Nasopharyngeal carcinoma cell line (C666-1) consistently harbouring Epstein-Barr virus.[J].Int J Cancer,1999,83(1):121-6.
[22] Tso KK,Yip KY,Mak CK,et al.Complete genomic sequence of Epstein-Barr virus in nasopharyngeal carcinoma cell line C666-1[J].Infect Agent Cancer,2013,8(1):29.
[23] Lin Z,Wang X,Strong MJ,et al.Whole-genome sequencing of the akata and mutu epstein-barr virus strains[J].J Virol,2012,87(2):1172-82.
[24] Tong AH,Lin CH.Genomic sequencing and comparative analysis of Epstein-barr virus genome isolated from primary nasopharyngeal carcinoma biopsy[J].PLoS One,2012,7(5):e36939.
[25] Simbiri KO,Smith NA,Otieno R,et al.Epstein-barr virus genetic variation in lymphoblastoid cell lines derived from kenyan pediatric population[J].PLoS One,2015,10(5):e0125420.
[26] Tsai MH,Raykova A,Klinke O,et al.Spontaneous lytic replication and epitheliotropism define an Epstein-barr virus strain found in carcinomas[J].Cell Rep,2013,5(2):458-70.
[27] Delecluse HJ,Hilsendegen T,Pich D,et al.Propagation and recovery of intact,infectious Epstein-Barr virus from prokaryotic to human cells[J].Proc Natl Acad Sci USA,1998,95(14):8245-50.
[28] 喻正源.全基因组测序与病毒捕获测序技术探讨EB病毒进化及整合规律的初步研究[J].博士,2013.
[29] 张鑫,李敏,张学军.全基因组外显子测序及其应用[J].HEREDITAS (Beijing),2011,8(33):847-56.
[30] Kwok H,Wu CW,Palser AL,et al.Genomic diversity of Epstein-barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples[J].J Virol,2014,88(18):10662-72.
[31] Palser AL,Grayson NE,White RE,et al.Genome diversity of Epstein-barr virus from multiple tumor types and normal infection[J].J Virol,2015,89(10):5222-37.
[32] Kwok H,Chiang A.From Conventional to next generation sequencing of Epstein-barr virus genomes[J].Viruses,2016,8(3):60.
[33] 郑钢.基于下一代测序的短序列匹配与支架算法研究[D].信阳师范学院,2015.
[34] Li H,Durbin R.Fast and accurate short read alignment with Burrows-Wheeler transform[J].Bioinformatics,2009,25(14):1754-60.
[35] Langmead B,Trapnell C,Pop M,et al.Ultrafast and memory-efficient alignment of short DNA sequences to the human genome[J].Genome Biol,2009,10(3):R25.
[36] Li R,Yu C,Li Y,et al.SOAP2:an improved ultrafast tool for short read alignment[J].Bioinformatics,2009,25(15):1966-7.
[37] Huang Q,Petros AM,Virgin HW,et al.Solution structure of the BHRF1 protein from Epstein-barr virus,a homolog of human Bcl-2[J].J Mol Biol,2003,332(5):1123-30.
[38] Stewart JP.The interleukin-10 homolog encoded by Epstein-barr virus-specific cytotoxic T cell and HLA-unrestricted virus enhances the reactivation killer cell responses[J].Virology,1992,191(2):773-82.
[39] 郑广勇,杨桢,曹瑞芳,等.宏基因组大数据分析的质量控制流程规范[J].大数据,2018,4(03):3-12.
[40] Ewing B,Hillier L,Wendl MC,et al.Base-calling of automated sequencer traces usingphred.I[J].Genome Res,1998,8(3):175-85.
[41] Wingett SW.FastQ Screen:A tool for multi-genome mapping and quality control[J].F1000Res,2018(7):1338.
[42] 袁易,王铭杰,张欣欣.第三代测序技术的主要特点及其在病毒基因组研究中的应用[J].微生物与感染,2016,11(06):380-4.
[43] Lei H,Li T,Hung G,et al.Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology[J].BMC genomics,2013,14(1):804.
[44] Song K,Yang S,Hwang J,et al.The full-length DNA sequence of Epstein barr virus from a human gastric carcinoma cell line,SNU-719[J].Virus Genes,2015,51(3):329-37.
[45] Santpere G,Darre F,Blanco S,et al.Genome-wide analysis of wild-type Epstein-barr virus genomes derived from healthy individuals of the 1000 genomes project[J].Genome Biol Evol,2014,6(4):846-60.
[46] Lei H,Li T,Li B,et al.Epstein-barr virus from burkitt lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations[J].Sci Rep,2015,5:16706.
[47] Simbiri KO,Smith NA,Otieno R,et al.Epstein-barr virus genetic variation in lymphoblastoid cell lines derived from kenyan pediatric population[J].PLoS One,10(5):e0125420.
[48] Liu Y,Yang W,Pan Y,et al.Genome-wide analysis of Epstein-barr virus (EBV) isolated from EBV-associated gastric carcinoma (EBVaGC)[J].Oncotarget,2016,7(4):4903-14.
[49] Tu C,Zeng Z,Qi P,et al.Genome-wide analysis of 18 Epstein-barr viruses isolated from primary nasopharyngeal carcinoma biopsy specimens[J].J Virol,2017,91(17):e00301-17.
[50] Wang S,Xiong H,Yan S,et al.Identification and characterization of Epstein-barr virus genomes in lung carcinoma biopsy samples by next-generation sequencing technology[J].Sci Rep,2016,6:26156.