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Article ; Online: Essential role of inverted repeat in Epstein-Barr virus IR-1 in B cell transformation; geographical variation of the viral genome.

Bridges, Ray / Correia, Samantha / Wegner, Fanny / Venturini, Cristina / Palser, Anne / White, Robert E / Kellam, Paul / Breuer, Judith / Farrell, Paul J

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2019 Volume 374, Issue 1773, Page(s) 20180299

Abstract: Many regions of the Epstein-Barr virus (EBV) genome, repeated and unique sequences, contribute to the geographical variation observed between strains. Here we use a large alignment of curated EBV genome sequences to identify major sites of variation in ... ...

Abstract	Many regions of the Epstein-Barr virus (EBV) genome, repeated and unique sequences, contribute to the geographical variation observed between strains. Here we use a large alignment of curated EBV genome sequences to identify major sites of variation in the genome of type 1 EBV strains; the CAO deletion in latent membrane protein 1 (LMP1) is the most frequent major indel present in the unique regions of EBV strains from various parts of the world. Principal component analysis was used to identify patterns of sequence variation and nucleotide positions in the sequences that can distinguish EBV from some different geographical regions. Viral genome sequence variation also affects interpretation of genetic content; known genes, origins of replication and gene expression control regions explain most of the viral genome but there are still a few sections of unknown function. One of these EBV genome regions contains a large inverted repeat sequence (invR) within the IR-1 major internal repeat array. We deleted this invR sequence and showed that this abolished the ability of the virus to transform human B cells into lymphoblastoid cell lines. This article is part of the theme issue 'Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses'.
MeSH term(s)	Epstein-Barr Virus Infections/virology ; Genetic Variation ; Genome, Viral/genetics ; Geography ; Herpesvirus 4, Human/genetics ; Humans ; Inverted Repeat Sequences ; Viral Proteins/metabolism
Chemical Substances	Viral Proteins
Language	English
Publishing date	2019-04-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2018.0299
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Article ; Online: Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.

Ba Abdullah, Mohammed M / Palermo, Richard D / Palser, Anne L / Grayson, Nicholas E / Kellam, Paul / Correia, Samantha / Szymula, Agnieszka / White, Robert E

Journal of virology

2017 Volume 91, Issue 23

Abstract: Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified through both coevolution with its host and genetic exchange between virus strains. Sequence ... ...

Abstract	Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified through both coevolution with its host and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging because of the large number and lengths of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat 1 of EBV (IR1; also known as the BamW repeats) for more than 70 strains. The diversity of the latency protein EBV nuclear antigen leader protein (EBNA-LP) resides predominantly within the exons downstream of IR1. The integrity of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions truncating IR1 always spare BWRF1. Conserved regions include the IR1 latency promoter (Wp) and one zone upstream of and two within BWRF1. IR1 is heterogeneous in 70% of strains, and this heterogeneity arises from sequence exchange between strains as well as from spontaneous mutation, with interstrain recombination being more common in tumor-derived viruses. This genetic exchange often incorporates regions of <1 kb, and allelic gene conversion changes the frequency of small regions within the repeat but not close to the flanks. These observations suggest that IR1-and, by extension, EBV-diversifies through both recombination and breakpoint repair, while concerted evolution of IR1 is driven by gene conversion of small regions. Finally, the prototype EBV strain B95-8 contains four nonconsensus variants within a single IR1 repeat unit, including a stop codon in the EBNA-LP gene. Repairing IR1 improves EBNA-LP levels and the quality of transformation by the B95-8 bacterial artificial chromosome (BAC).
MeSH term(s)	Codon, Terminator ; Epstein-Barr Virus Nuclear Antigens/genetics ; Evolution, Molecular ; Gene Conversion ; Genes, Viral ; Genetic Variation ; Genome, Viral ; Herpesvirus 4, Human/genetics ; Herpesvirus 4, Human/metabolism ; High-Throughput Nucleotide Sequencing ; Humans ; Mutation ; Open Reading Frames ; Promoter Regions, Genetic ; Repetitive Sequences, Nucleic Acid
Chemical Substances	Codon, Terminator ; Epstein-Barr Virus Nuclear Antigens
Language	English
Publishing date	2017-11-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00920-17
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Article ; Online: Sequence Variation of Epstein-Barr Virus: Viral Types, Geography, Codon Usage, and Diseases.

Correia, Samantha / Bridges, Ray / Wegner, Fanny / Venturini, Cristina / Palser, Anne / Middeldorp, Jaap M / Cohen, Jeffrey I / Lorenzetti, Mario A / Bassano, Irene / White, Robert E / Kellam, Paul / Breuer, Judith / Farrell, Paul J

Journal of virology

2018 Volume 92, Issue 22

Abstract: One hundred thirty-eight new Epstein-Barr virus (EBV) genome sequences have been determined. One hundred twenty-five of these and 116 from previous reports were combined to produce a multiple-sequence alignment of 241 EBV genomes, which we have used to ... ...

Abstract	One hundred thirty-eight new Epstein-Barr virus (EBV) genome sequences have been determined. One hundred twenty-five of these and 116 from previous reports were combined to produce a multiple-sequence alignment of 241 EBV genomes, which we have used to analyze variation within the viral genome. The type 1/type 2 classification of EBV remains the major form of variation and is defined mostly by EBNA2 and EBNA3, but the type 2 single-nucleotide polymorphisms (SNPs) at the EBNA3 locus extend into the adjacent gp350 and gp42 genes, whose products mediate infection of B cells by EBV. A small insertion within the BART microRNA region of the genome was present in 21 EBV strains. EBV from saliva of U.S. patients with chronic active EBV infection aligned with the wild-type EBV genome with no evidence of WZhet rearrangements. The V3 polymorphism in the Zp promoter for BZLF1 was found to be frequent in nasopharyngeal carcinoma cases from both Hong Kong and Indonesia. Codon usage was found to differ between latent and lytic cycle EBV genes, and the main forms of variation of the EBNA1 protein have been identified.
MeSH term(s)	Base Sequence ; Burkitt Lymphoma/genetics ; Epstein-Barr Virus Nuclear Antigens/genetics ; Genome, Viral/genetics ; Herpesvirus 4, Human/genetics ; Humans ; Infectious Mononucleosis/genetics ; Polymorphism, Single Nucleotide/genetics ; Promoter Regions, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Stomach Neoplasms/genetics ; Trans-Activators/genetics ; Viral Proteins/genetics
Chemical Substances	BZLF1 protein, Herpesvirus 4, Human ; EBNA-2 protein, Human herpesvirus 4 ; EBNA-3A antigen ; Epstein-Barr Virus Nuclear Antigens ; Trans-Activators ; Viral Proteins
Language	English
Publishing date	2018-10-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01132-18
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Article ; Online: Natural Variation of Epstein-Barr Virus Genes, Proteins, and Primary MicroRNA.

Correia, Samantha / Palser, Anne / Elgueta Karstegl, Claudio / Middeldorp, Jaap M / Ramayanti, Octavia / Cohen, Jeffrey I / Hildesheim, Allan / Fellner, Maria Dolores / Wiels, Joelle / White, Robert E / Kellam, Paul / Farrell, Paul J

Journal of virology

2017 Volume 91, Issue 15

Abstract: Viral gene sequences from an enlarged set of about 200 Epstein-Barr virus (EBV) strains, including many primary isolates, have been used to investigate variation in key viral genetic regions, particularly LMP1, Zp, gp350, EBNA1, and the BART microRNA ( ... ...

Abstract	Viral gene sequences from an enlarged set of about 200 Epstein-Barr virus (EBV) strains, including many primary isolates, have been used to investigate variation in key viral genetic regions, particularly LMP1, Zp, gp350, EBNA1, and the BART microRNA (miRNA) cluster 2. Determination of type 1 and type 2 EBV in saliva samples from people from a wide range of geographic and ethnic backgrounds demonstrates a small percentage of healthy white Caucasian British people carrying predominantly type 2 EBV. Linkage of Zp and gp350 variants to type 2 EBV is likely to be due to their genes being adjacent to the EBNA3 locus, which is one of the major determinants of the type 1/type 2 distinction. A novel classification of EBNA1 DNA binding domains, named QCIGP, results from phylogeny analysis of their protein sequences but is not linked to the type 1/type 2 classification. The BART cluster 2 miRNA region is classified into three major variants through single-nucleotide polymorphisms (SNPs) in the primary miRNA outside the mature miRNA sequences. These SNPs can result in altered levels of expression of some miRNAs from the BART variant frequently present in Chinese and Indonesian nasopharyngeal carcinoma (NPC) samples. The EBV genetic variants identified here provide a basis for future, more directed analysis of association of specific EBV variations with EBV biology and EBV-associated diseases.
MeSH term(s)	Epstein-Barr Virus Infections/epidemiology ; Epstein-Barr Virus Infections/virology ; Ethnicity ; Genetic Variation ; Genotype ; Geography ; Herpesvirus 4, Human/classification ; Herpesvirus 4, Human/genetics ; Herpesvirus 4, Human/isolation & purification ; Humans ; London ; MicroRNAs/genetics ; Molecular Epidemiology ; Saliva/virology ; Students ; United States ; Viral Proteins/genetics ; Volunteers
Chemical Substances	MicroRNAs ; Viral Proteins
Language	English
Publishing date	2017-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00375-17
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Article ; Online: A Conserved Interaction between a C-Terminal Motif in Norovirus VPg and the HEAT-1 Domain of eIF4G Is Essential for Translation Initiation.

Leen, Eoin N / Sorgeloos, Frédéric / Correia, Samantha / Chaudhry, Yasmin / Cannac, Fabien / Pastore, Chiara / Xu, Yingqi / Graham, Stephen C / Matthews, Stephen J / Goodfellow, Ian G / Curry, Stephen

PLoS pathogens

2016 Volume 12, Issue 1, Page(s) e1005379

Abstract: Translation initiation is a critical early step in the replication cycle of the positive-sense, single-stranded RNA genome of noroviruses, a major cause of gastroenteritis in humans. Norovirus RNA, which has neither a 5´ m7G cap nor an internal ribosome ... ...

Abstract	Translation initiation is a critical early step in the replication cycle of the positive-sense, single-stranded RNA genome of noroviruses, a major cause of gastroenteritis in humans. Norovirus RNA, which has neither a 5´ m7G cap nor an internal ribosome entry site (IRES), adopts an unusual mechanism to initiate protein synthesis that relies on interactions between the VPg protein covalently attached to the 5´-end of the viral RNA and eukaryotic initiation factors (eIFs) in the host cell. For murine norovirus (MNV) we previously showed that VPg binds to the middle fragment of eIF4G (4GM; residues 652-1132). Here we have used pull-down assays, fluorescence anisotropy, and isothermal titration calorimetry (ITC) to demonstrate that a stretch of ~20 amino acids at the C terminus of MNV VPg mediates direct and specific binding to the HEAT-1 domain within the 4GM fragment of eIF4G. Our analysis further reveals that the MNV C terminus binds to eIF4G HEAT-1 via a motif that is conserved in all known noroviruses. Fine mutagenic mapping suggests that the MNV VPg C terminus may interact with eIF4G in a helical conformation. NMR spectroscopy was used to define the VPg binding site on eIF4G HEAT-1, which was confirmed by mutagenesis and binding assays. We have found that this site is non-overlapping with the binding site for eIF4A on eIF4G HEAT-1 by demonstrating that norovirus VPg can form ternary VPg-eIF4G-eIF4A complexes. The functional significance of the VPg-eIF4G interaction was shown by the ability of fusion proteins containing the C-terminal peptide of MNV VPg to inhibit in vitro translation of norovirus RNA but not cap- or IRES-dependent translation. These observations define important structural details of a functional interaction between norovirus VPg and eIF4G and reveal a binding interface that might be exploited as a target for antiviral therapy.
MeSH term(s)	Amino Acid Motifs ; Animals ; Calorimetry ; Cell Line ; Chromatography, Gel ; Eukaryotic Initiation Factor-4G/metabolism ; Immunoprecipitation ; Magnetic Resonance Spectroscopy ; Mice ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Norovirus/physiology ; Peptide Chain Initiation, Translational/physiology ; Protein Structure, Secondary ; Viral Proteins/metabolism
Chemical Substances	Eukaryotic Initiation Factor-4G ; Viral Proteins
Language	English
Publishing date	2016-01-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1005379
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Correction: A Conserved Interaction between a C-Terminal Motif in Norovirus VPg and the HEAT-1 Domain of eIF4G Is Essential for Translation Initiation.

PLoS pathogens

2016 Volume 12, Issue 3, Page(s) e1005509

Language	English
Publishing date	2016-03-11
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1005509
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Article ; Online: Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection.

Palser, Anne L / Grayson, Nicholas E / White, Robert E / Corton, Craig / Correia, Samantha / Ba Abdullah, Mohammed M / Watson, Simon J / Cotten, Matthew / Arrand, John R / Murray, Paul G / Allday, Martin J / Rickinson, Alan B / Young, Lawrence S / Farrell, Paul J / Kellam, Paul

Journal of virology

2015 Volume 89, Issue 10, Page(s) 5222–5237

Abstract: Unlabelled: Epstein-Barr virus (EBV) infects most of the world's population and is causally associated with several human cancers, but little is known about how EBV genetic variation might influence infection or EBV-associated disease. There are ... ...

Abstract	Unlabelled: Epstein-Barr virus (EBV) infects most of the world's population and is causally associated with several human cancers, but little is known about how EBV genetic variation might influence infection or EBV-associated disease. There are currently no published wild-type EBV genome sequences from a healthy individual and very few genomes from EBV-associated diseases. We have sequenced 71 geographically distinct EBV strains from cell lines, multiple types of primary tumor, and blood samples and the first EBV genome from the saliva of a healthy carrier. We show that the established genome map of EBV accurately represents all strains sequenced, but novel deletions are present in a few isolates. We have increased the number of type 2 EBV genomes sequenced from one to 12 and establish that the type 1/type 2 classification is a major feature of EBV genome variation, defined almost exclusively by variation of EBNA2 and EBNA3 genes, but geographic variation is also present. Single nucleotide polymorphism (SNP) density varies substantially across all known open reading frames and is highest in latency-associated genes. Some T-cell epitope sequences in EBNA3 genes show extensive variation across strains, and we identify codons under positive selection, both important considerations for the development of vaccines and T-cell therapy. We also provide new evidence for recombination between strains, which provides a further mechanism for the generation of diversity. Our results provide the first global view of EBV sequence variation and demonstrate an effective method for sequencing large numbers of genomes to further understand the genetics of EBV infection. Importance: Most people in the world are infected by Epstein-Barr virus (EBV), and it causes several human diseases, which occur at very different rates in different parts of the world and are linked to host immune system variation. Natural variation in EBV DNA sequence may be important for normal infection and for causing disease. Here we used rapid, cost-effective sequencing to determine 71 new EBV sequences from different sample types and locations worldwide. We showed geographic variation in EBV genomes and identified the most variable parts of the genome. We identified protein sequences that seem to have been selected by the host immune system and detected variability in known immune epitopes. This gives the first overview of EBV genome variation, important for designing vaccines and immune therapy for EBV, and provides techniques to investigate relationships between viral sequence variation and EBV-associated diseases.
MeSH term(s)	Amino Acid Sequence ; Antigens, Viral/genetics ; Carrier State/virology ; Cell Line, Tumor ; DNA, Viral/genetics ; Epitopes, T-Lymphocyte/genetics ; Epstein-Barr Virus Infections/virology ; Epstein-Barr Virus Nuclear Antigens/genetics ; Genetic Variation ; Genome, Viral ; Herpesvirus 4, Human/classification ; Herpesvirus 4, Human/genetics ; Herpesvirus 4, Human/isolation & purification ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Viral Matrix Proteins/genetics
Chemical Substances	Antigens, Viral ; DNA, Viral ; EBV-associated membrane antigen, Epstein-Barr virus ; Epitopes, T-Lymphocyte ; Epstein-Barr Virus Nuclear Antigens ; Viral Matrix Proteins
Language	English
Publishing date	2015-03-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.03614-14
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Essential role of inverted repeat in Epstein-Barr virus IR-1 in B cell transformation; geographical variation of the viral genome.

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Article ; Online: Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.

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Article ; Online: Sequence Variation of Epstein-Barr Virus: Viral Types, Geography, Codon Usage, and Diseases.

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In stock of ZB MED Cologne/Königswinter

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Article ; Online: Natural Variation of Epstein-Barr Virus Genes, Proteins, and Primary MicroRNA.

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Article ; Online: A Conserved Interaction between a C-Terminal Motif in Norovirus VPg and the HEAT-1 Domain of eIF4G Is Essential for Translation Initiation.

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Article ; Online: Correction: A Conserved Interaction between a C-Terminal Motif in Norovirus VPg and the HEAT-1 Domain of eIF4G Is Essential for Translation Initiation.

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Article ; Online: Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection.

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