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      Viral and host factors drive a type 1 Epstein–Barr virus spontaneous lytic phenotype

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          ABSTRACT

          Epstein–Barr virus (EBV) is a cancer and autoimmune disease-associated gamma-herpesvirus that infects the majority of adults worldwide. After initial infection, EBV generally maintains a latent state in the host with minimal viral gene expression. However, aberrations in this prototypical latent viral state leading to increased lytic replication can cause upregulation of oncogenic factors, promoting EBV-associated diseases. For example, nasopharyngeal carcinoma and post-transplant lymphoproliferative disease have strong associations with EBV lytic replication. Another EBV-associated disease, endemic Burkitt lymphoma (BL), is an extremely fast-growing cancer found primarily in children in malaria-endemic regions of Sub-Saharan Africa. Nearly all endemic BL tumors are infected with EBV and the hallmark of the disease is high levels of oncogenic c-Myc expression due to an immunoglobulin/ Myc translocation. In this study, we describe spontaneous lytic phenotypes in EBV strains isolated from Kenyan BL patient tumors. We specifically focus on a novel Type 1 spontaneously lytic EBV strain and describe viral and host factors that could contribute to this phenotype. We found that cells infected with spontaneous lytic strains have lower c-Myc protein stability and express high levels of the plasma cell marker SLAMF7. Additionally, spontaneous lytic strains have altered latency states, which appear to further promote their lytic phenotypes. The isolation of spontaneously lytic EBV strains from endemic BL tumors provides more evidence that EBV may not maintain a prototypically latent state in patients with EBV-associated diseases and raises the possibility that promiscuous lytic activity may contribute to the formation of these diseases.

          IMPORTANCE

          Epstein–Barr virus (EBV) infects over 95% of adults worldwide. Given its connection to various cancers and autoimmune disorders, it is important to understand the mechanisms by which infection with EBV can lead to these diseases. In this study, we describe an unusual spontaneous lytic phenotype in EBV strains isolated from Kenyan endemic Burkitt lymphoma patients. Because lytic replication of EBV has been linked to the pathogenesis of various diseases, these data could illuminate viral and host factors involved in this process.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

              Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT2, for representing and searching an expanded model of the human reference genome, in which a large catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate two initial applications of HISAT2: HLA typing, a critical need in human organ transplantation, and DNA fingerprinting, widely used in forensics. These applications are part of HISAT-genotype, with performance not only surpassing earlier computational methods, but matching or exceeding the accuracy of laboratory-based assays.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: ValidationRole: VisualizationRole: Writing – review and editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Resources
                Role: ResourcesRole: Writing – review and editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Writing – review and editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review and editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – review and editing
                Role: Editor
                Role: Invited Editor
                Journal
                mBio
                mBio
                mbio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                Nov-Dec 2023
                16 November 2023
                16 November 2023
                : 14
                : 6
                : e02204-23
                Affiliations
                [1 ]Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine; , Durham, North Carolina, USA
                [2 ]Department of Pathology and Laboratory Medicine, Brown University; , Providence, Rhode Island, USA
                [3 ]Center for Global Health Research, Kenya Medical Research Institute; , Kisumu, Kenya
                [4 ]Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School; , Worcester, Massachusetts, USA
                Columbia University Medical Center; , New York, New York, USA
                Harvard Medical School, Brigham and Women's Hospital; , Boston, Massachusetts, USA
                Author notes
                Address correspondence to Micah A. Luftig, micah.luftig@ 123456duke.edu

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0002-0044-2664
                https://orcid.org/0000-0003-1113-2829
                https://orcid.org/0000-0002-2964-1907
                Article
                02204-23 mbio.02204-23
                10.1128/mbio.02204-23
                10746244
                37971257
                f4607fc5-62d0-49e9-a54e-923ffa3a50ce
                Copyright © 2023 Willard et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 22 August 2023
                : 21 September 2023
                Page count
                supplementary-material: 10, authors: 7, Figures: 8, Tables: 2, References: 69, Pages: 26, Words: 14067
                Funding
                Funded by: HHS | NIH | National Cancer Institute (NCI);
                Award ID: R01 CA234348
                Award Recipient :
                Funded by: HHS | NIH | National Cancer Institute (NCI);
                Award ID: R01 CA189806
                Award Recipient :
                Funded by: National Science Foundation (NSF);
                Award ID: GRFP 1644868
                Award Recipient :
                Categories
                Research Article
                virology, Virology
                Custom metadata
                November/December 2023

                Life sciences
                epstein–barr virus,herpesvirus,lytic replication,burkitt lymphoma
                Life sciences
                epstein–barr virus, herpesvirus, lytic replication, burkitt lymphoma

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