1
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Flores Cortes E, Saddoris SM, Owens AK, Gibeault R, Depledge DP, Schang LM. Histone H2A variant H2A.B is enriched in transcriptionally active and replicating HSV-1 lytic chromatin. J Virol 2024; 98:e0201523. [PMID: 38451083 PMCID: PMC11019955 DOI: 10.1128/jvi.02015-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections but the precise mechanisms are not fully defined. Nucleosomes are dynamic: they slide, breathe, assemble, and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent, whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X, and macroH2A were enhanced in infected cells, whereas those of H2A.B were uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, as well as ectopic and endogenous H2B were assembled into HSV-1 chromatin evenly throughout the genome but canonical H2A was relatively depleted whereas H2A.B was enriched, particularly in the most dynamic viral chromatin. When viral transcription and DNA replication were restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants. IMPORTANCE Herpes simplex virus 1 (HSV-1) transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed epigenetic mechanisms of regulation of HSV-1 transcription have not been fully characterized and may differ from those regulating cellular transcription. Whereas lytic HSV-1 chromatin is unusually dynamic, latent silenced HSV-1 chromatin is not. The mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment of the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding of its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
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Affiliation(s)
- Esteban Flores Cortes
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Sarah M. Saddoris
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Arryn K. Owens
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Rebecca Gibeault
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel P. Depledge
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
| | - Luis M. Schang
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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2
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Ouwendijk WJD, Roychoudhury P, Cunningham AL, Jerome KR, Koelle DM, Kinchington PR, Mohr I, Wilson AC, Verjans GGMGM, Depledge DP. Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice. J Virol 2024; 98:e0185823. [PMID: 38445887 PMCID: PMC11019907 DOI: 10.1128/jvi.01858-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Most individuals are latently infected with herpes simplex virus type 1 (HSV-1), and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent HSV-1 is also present in immune cells recovered from the ganglia of experimentally infected mice. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for that conclusion. Unexpectedly, off-target priming in 3' scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1 latency-associated transcript (LAT) intronic RNAs. However, LAT reads were near-exclusively detected in mixed populations of cells undergoing cell death. Specific loss of HSV-1 LAT and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained using compromised scRNA-Seq datasets.IMPORTANCEMost people are infected with herpes simplex virus type 1 (HSV-1) during their life. Once infected, the virus generally remains in a latent (silent) state, hiding within the neurons of peripheral ganglia. Periodic reactivation (reawakening) of the virus may cause fresh diseases such as cold sores. A recent study using single-cell RNA sequencing (scRNA-Seq) proposed that HSV-1 can also establish latency in the immune cells of mice, challenging existing dogma. We reanalyzed the data from that study and identified several flaws in the methodologies and analyses performed that invalidate the published conclusions. Specifically, we showed that the methodologies used resulted in widespread destruction of neurons which resulted in the presence of contaminants that confound the data analysis. We thus conclude that there remains little to no evidence for HSV-1 latency in immune cells.
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Affiliation(s)
- Werner J. D. Ouwendijk
- HerpesLabNL, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David M. Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Translational Research, Benaroya Research Institute, Seattle, Washington, USA
| | - Paul R. Kinchington
- Department of Ophthalmology and of Molecular Microbiology and Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | | | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF) partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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3
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Abebe JS, Alwie Y, Fuhrmann E, Leins J, Mai J, Verstraten R, Schreiner S, Wilson AC, Depledge DP. Nanopore Guided Annotation of Transcriptome Architectures. bioRxiv 2024:2024.04.02.587744. [PMID: 38617228 PMCID: PMC11014626 DOI: 10.1101/2024.04.02.587744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
High-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs, without recoding or amplification bias, and resulting data may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails on individual RNA molecules. Existing software solutions for generating high-resolution transcriptome annotations are poorly suited to small gene dense organisms such as viruses due to the challenge of identifying distinct transcript isoforms where alternative splicing and overlapping RNAs are prevalent. To resolve this, we identified key characteristics of DRS datasets and developed a novel approach to transcriptome. We demonstrate, using a combination of synthetic and original datasets, that our novel approach yields a high level of precision and recall when reconstructing both gene sparse and gene dense transcriptomes from DRS datasets. We further apply this approach to generate a new high resolution transcriptome annotation of the neglected pathogen human adenovirus type F 41 for which we identify 77 distinct transcripts encoding at least 23 different proteins.
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Affiliation(s)
- Jonathan S. Abebe
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Yasmine Alwie
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Erik Fuhrmann
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Jonas Leins
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Julia Mai
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Ruth Verstraten
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Sabrina Schreiner
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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4
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Krueger J, Preusse M, Oswaldo Gomez N, Frommeyer YN, Doberenz S, Lorenz A, Kordes A, Grobe S, Müsken M, Depledge DP, Svensson SL, Weiss S, Kaever V, Pich A, Sharma CM, Ignatova Z, Häussler S. tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2024; 121:e2312874121. [PMID: 38451943 PMCID: PMC10945773 DOI: 10.1073/pnas.2312874121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/29/2023] [Indexed: 03/09/2024] Open
Abstract
The success of bacterial pathogens depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered, and incompletely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that the enzymatic activity of GidA leads to the introduction of a carboxymethylaminomethyl modification in selected tRNAs. Modifications at the wobble uridine base (cmnm5U34) of the anticodon drives translation of transcripts containing rare codons. Specifically, in P. aeruginosa the presence of GidA-dependent tRNA modifications modulates expression of genes encoding virulence regulators, leading to a cellular proteomic shift toward pathogenic and well-adapted physiological states. Our approach of profiling the consequences of chemical tRNA modifications is general in concept. It provides a paradigm of how environmentally driven tRNA modifications govern gene expression programs and regulate phenotypic outcomes responsible for bacterial adaption to challenging habitats prevailing in the host niche.
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Affiliation(s)
- Jonas Krueger
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Research Core Unit Proteomics and Institute for Toxicology, Hannover Medical School, Hannover30625, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Nicolas Oswaldo Gomez
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Yannick Noah Frommeyer
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
| | - Sebastian Doberenz
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
| | - Anne Lorenz
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
| | - Adrian Kordes
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
| | - Svenja Grobe
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover 30625, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig38124, Germany
| | - Daniel P. Depledge
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
- Institute of Virology, Hannover Medical School, Hannover30625, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Hannover30625, Germany
| | - Sarah L. Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Siegfried Weiss
- Institute of Immunology, Medical School Hannover, Hannover30625, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover 30625, Germany
| | - Andreas Pich
- Research Core Unit Proteomics and Institute for Toxicology, Hannover Medical School, Hannover30625, Germany
| | - Cynthia M. Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg97080, Germany
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University Hamburg, 20146, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, Center of Clinical and Experimental Infection Research (TWINCORE), a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover30625, Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, 38124Braunschweig, Germany
- Cluster of Excellence “Resolving Infection susceptibility” (RESIST), Hannover Medical School, Hannover30625, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital—Rigshospitalet, Copenhagen2100, Denmark
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5
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Flores E, Saddoris SM, Owens AK, Gibeault R, Depledge DP, Schang LM. Histone H2A variant H2A.B is enriched in transcriptionally active HSV-1 lytic chromatin. bioRxiv 2023:2023.12.22.573075. [PMID: 38187672 PMCID: PMC10769327 DOI: 10.1101/2023.12.22.573075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections, but the precise mechanisms are not fully defined. Nucleosomes are dynamic; they slide, breathe, assemble and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X and macroH2A were enhanced in infected cells, whereas those of H2A.B uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, ectopic, and endogenous H2B, were assembled into HSV-1 chromatin evenly throughout the genome, but canonical H2A was relatively depleted from the viral chromatin whereas H2A.B was enriched in the most dynamic viral chromatin. When viral transcription was restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency, and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants. Importance HSV-1 transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed mechanisms of regulation of HSV-1 transcription by epigenetics have not been fully characterized and may differ from those regulating cellular transcription. In particular, the lytic HSV-1 chromatin is unusually dynamic, whereas the latent silenced one is not, but the mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment on the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding for its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
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6
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Burgess HM, Grande R, Riccio S, Dinesh I, Winkler GS, Depledge DP, Mohr I. CCR4-NOT differentially controls host versus virus poly(a)-tail length and regulates HCMV infection. EMBO Rep 2023; 24:e56327. [PMID: 37846490 PMCID: PMC10702830 DOI: 10.15252/embr.202256327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/18/2023] Open
Abstract
Unlike most RNA and DNA viruses that broadly stimulate mRNA decay and interfere with host gene expression, human cytomegalovirus (HCMV) extensively remodels the host translatome without producing an mRNA decay enzyme. By performing a targeted loss-of-function screen in primary human fibroblasts, we here identify the host CCR4-NOT deadenylase complex members CNOT1 and CNOT3 as unexpected pro-viral host factors that selectively regulate HCMV reproduction. We find that the scaffold subunit CNOT1 is specifically required for late viral gene expression and genome-wide host responses in CCR4-NOT-disrupted cells. By profiling poly(A)-tail lengths of individual HCMV and host mRNAs using nanopore direct RNA sequencing, we reveal poly(A)-tails of viral messages to be markedly longer than those of cellular mRNAs and significantly less sensitive to CCR4-NOT disruption. Our data establish that mRNA deadenylation by host CCR4-NOT is critical for productive HCMV replication and define a new mechanism whereby herpesvirus infection subverts cellular mRNA metabolism to remodel the gene expression landscape of the infected cell. Moreover, we expose an unanticipated host factor with potential to become a therapeutic anti-HCMV target.
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Affiliation(s)
- Hannah M Burgess
- Department of Microbial SciencesUniversity of SurreyGuildfordUK
- Department of Microbiology, School of MedicineNew York UniversityNew YorkNYUSA
| | - Rebecca Grande
- Department of Microbiology, School of MedicineNew York UniversityNew YorkNYUSA
| | - Sofia Riccio
- Department of Microbial SciencesUniversity of SurreyGuildfordUK
| | - Ikshitaa Dinesh
- Department of Microbial SciencesUniversity of SurreyGuildfordUK
| | | | - Daniel P Depledge
- Department of Microbiology, School of MedicineNew York UniversityNew YorkNYUSA
- Institute of VirologyHannover Medical SchoolHannoverGermany
- German Center for Infection Research (DZIF), partner site Hannover‐BraunschweigHannoverGermany
| | - Ian Mohr
- Department of Microbiology, School of MedicineNew York UniversityNew YorkNYUSA
- Laura and Isaac Perlmutter Cancer Institute, School of MedicineNew York UniversityNew YorkNYUSA
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7
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Ouwendijk WJ, Roychoudhury P, Cunningham AL, Jerome KR, Koelle DM, Kinchington PR, Mohr I, Wilson AC, Verjans GM, Depledge DP. Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice. bioRxiv 2023:2023.07.17.549345. [PMID: 37503290 PMCID: PMC10370134 DOI: 10.1101/2023.07.17.549345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Most individuals are latently infected with herpes simplex virus type 1 (HSV-1) and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent virus is also present in immune cells recovered from ganglia in a mouse model used for studying latency. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for this conclusion. Unexpectedly, off-target priming in 3' scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1 latency-associated transcript (LAT) intronic RNAs. However, LAT reads were nearexclusively detected in a mixed population of cells undergoing cell death. Specific loss of HSV1 LAT and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained by inaccuracies in the data analyses.
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Affiliation(s)
- Werner J.D. Ouwendijk
- HerpesLabNL, Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - David M. Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
- Department of Global Health, University of Washington, Seattle, WA, 98195, USA
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, 98101, USA
| | - Paul R. Kinchington
- Department of Ophthalmology and of Molecular Microbiology and Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
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8
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Price AM, Steinbock RT, Lauman R, Charman M, Hayer KE, Kumar N, Halko E, Lum KK, Wei M, Wilson AC, Garcia BA, Depledge DP, Weitzman MD. Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts. PLoS Pathog 2022; 18:e1010797. [PMID: 36095031 PMCID: PMC9499273 DOI: 10.1371/journal.ppat.1010797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/22/2022] [Accepted: 08/05/2022] [Indexed: 01/07/2023] Open
Abstract
Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and RNA cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts that meet stringent criteria for expression. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORFs), six novel ORF-containing transcripts, and 15 transcripts encoding for messages that could alter protein functions through truncation or fusion of canonical ORFs. In addition, we detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking distinct gene transcription units. Among these chimeric proteins we detected an evolutionarily conserved protein containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies combined with mass spectrometry can reveal further complexity within viral transcriptomes and resulting proteomes.
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Affiliation(s)
- Alexander M. Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Robert T. Steinbock
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Richard Lauman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew Charman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Namrata Kumar
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Edwin Halko
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Krystal K. Lum
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Monica Wei
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York city, New York, United States of America
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York city, New York, United States of America
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Matthew D. Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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9
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Dochnal S, Merchant HY, Schinlever AR, Babnis A, Depledge DP, Wilson AC, Cliffe AR. DLK-Dependent Biphasic Reactivation of Herpes Simplex Virus Latency Established in the Absence of Antivirals. J Virol 2022; 96:e0050822. [PMID: 35608347 PMCID: PMC9215246 DOI: 10.1128/jvi.00508-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/30/2022] [Indexed: 01/07/2023] Open
Abstract
Understanding the molecular mechanisms of herpes simplex virus 1 (HSV-1) latent infection and reactivation in neurons requires the use of in vitro model systems. Establishing a quiescent infection in cultured neurons is problematic, as any infectious virus released can superinfect the cultures. Previous studies have used the viral DNA replication inhibitor acyclovir to prevent superinfection and promote latency establishment. Data from these previous models have shown that reactivation is biphasic, with an initial phase I expression of all classes of lytic genes, which occurs independently of histone demethylase activity and viral DNA replication but is dependent on the cell stress protein DLK. Here, we describe a new model system using HSV-1 Stayput-GFP, a reporter virus that is defective for cell-to-cell spread and establishes latent infections without the need for acyclovir. The establishment of a latent state requires a longer time frame than previous models using DNA replication inhibitors. This results in a decreased ability of the virus to reactivate using established inducers, and as such, a combination of reactivation triggers is required. Using this system, we demonstrate that biphasic reactivation occurs even when latency is established in the absence of acyclovir. Importantly, phase I lytic gene expression still occurs in a histone demethylase and viral DNA replication-independent manner and requires DLK activity. These data demonstrate that the two waves of viral gene expression following HSV-1 reactivation are independent of secondary infection and not unique to systems that require acyclovir to promote latency establishment. IMPORTANCE Herpes simplex virus-1 (HSV-1) enters a latent infection in neurons and periodically reactivates. Reactivation manifests as a variety of clinical symptoms. Studying latency and reactivation in vitro is invaluable, allowing the molecular mechanisms behind both processes to be targeted by therapeutics that reduce the clinical consequences. Here, we describe a novel in vitro model system using a cell-to-cell spread-defective HSV-1, known as Stayput-GFP, which allows for the study of latency and reactivation at the single neuron level. We anticipate this new model system will be an incredibly valuable tool for studying the establishment and reactivation of HSV-1 latent infection in vitro. Using this model, we find that initial reactivation events are dependent on cellular stress kinase DLK but independent of histone demethylase activity and viral DNA replication. Our data therefore further validate the essential role of DLK in mediating a wave of lytic gene expression unique to reactivation.
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Affiliation(s)
- Sara Dochnal
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Husain Y. Merchant
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Austin R. Schinlever
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Aleksandra Babnis
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Anna R. Cliffe
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
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10
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Abebe JS, Price AM, Hayer KE, Mohr I, Weitzman MD, Wilson AC, Depledge DP. DRUMMER—Rapid detection of RNA modifications through comparative nanopore sequencing. Bioinformatics 2022; 38:3113-3115. [PMID: 35426900 PMCID: PMC9154255 DOI: 10.1093/bioinformatics/btac274] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 11/23/2022] Open
Abstract
Motivation The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides. Results DRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity. Availability and implementation DRUMMER is written in Python 3 and is available as open source in the GitHub repository: https://github.com/DepledgeLab/DRUMMER. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jonathan S Abebe
- Department of Microbiology, New York University School of Medicine, New York, NY
| | - Alexander M Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, NY
| | - Matthew D Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY
| | - Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
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11
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Hu H, Srinivas KP, Wang S, Chao MV, Lionnet T, Mohr I, Wilson AC, Depledge DP, Huang TT. Single-cell transcriptomics identifies Gadd45b as a regulator of herpesvirus-reactivating neurons. EMBO Rep 2022; 23:e53543. [PMID: 34842321 PMCID: PMC8811635 DOI: 10.15252/embr.202153543] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 02/05/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful technique for dissecting the complexity of normal and diseased tissues, enabling characterization of cell diversity and heterogeneous phenotypic states in unprecedented detail. However, this technology has been underutilized for exploring the interactions between the host cell and viral pathogens in latently infected cells. Herein, we use scRNA-seq and single-molecule sensitivity fluorescent in situ hybridization (smFISH) technologies to investigate host single-cell transcriptome changes upon the reactivation of a human neurotropic virus, herpes simplex virus-1 (HSV-1). We identify the stress sensor growth arrest and DNA damage-inducible 45 beta (Gadd45b) as a critical antiviral host factor that regulates HSV-1 reactivation events in a subpopulation of latently infected primary neurons. We show that distinct subcellular localization of Gadd45b correlates with the viral late gene expression program, as well as the expression of the viral transcription factor, ICP4. We propose that a hallmark of a "successful" or "aborted" HSV-1 reactivation state in primary neurons is determined by a unique subcellular localization signature of the stress sensor Gadd45b.
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Affiliation(s)
- Hui‐Lan Hu
- Department of Biochemistry & Molecular PharmacologyNew York University School of MedicineNew YorkNYUSA
| | | | - Shuoshuo Wang
- Department of Cell BiologyInstitute for Systems GeneticsNew York University School of MedicineNew YorkNYUSA
| | - Moses V Chao
- Departments of Cell Biology, Physiology & Neuroscience, and PsychiatrySkirball Institute of Biomolecular MedicineNew York University School of MedicineNew YorkNYUSA
| | - Timothee Lionnet
- Department of Cell BiologyInstitute for Systems GeneticsNew York University School of MedicineNew YorkNYUSA
| | - Ian Mohr
- Department of MicrobiologyNew York University School of MedicineNew YorkNYUSA
| | - Angus C Wilson
- Department of MicrobiologyNew York University School of MedicineNew YorkNYUSA
| | - Daniel P Depledge
- Department of MedicineNew York University School of MedicineNew YorkNYUSA,Present address:
Institute of VirologyHannover Medical SchoolHannoverGermany
| | - Tony T Huang
- Department of Biochemistry & Molecular PharmacologyNew York University School of MedicineNew YorkNYUSA
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12
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Mavri M, Kubale V, Depledge DP, Zuo J, Huang CA, Breuer J, Vrecl M, Jarvis MA, Jovičić EJ, Petan T, Ehlers B, Rosenkilde MM, Spiess K. Epstein-Barr Virus-Encoded BILF1 Orthologues From Porcine Lymphotropic Herpesviruses Display Common Molecular Functionality. Front Endocrinol (Lausanne) 2022; 13:862940. [PMID: 35721730 PMCID: PMC9204316 DOI: 10.3389/fendo.2022.862940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Infection of immunosuppressed transplant patients with the human γ-herpesvirus Epstein-Barr virus (EBV) is associated with post-transplant lymphoproliferative disease (PTLD), an often fatal complication. Immunosuppressed miniature pigs infected with γ-herpesvirus porcine lymphotropic herpesvirus 1 (PLHV1) develop a similar disease, identifying pigs as a potential preclinical model for PTLD in humans. BILF1 is a G protein-coupled receptor (GPCR) encoded by EBV with constitutive activity linked to tumorigenesis and immunoevasive function downregulating MHC-I. In the present study, we compared BILF1-orthologues encoded by the three known PLHVs (PLHV1-3) with EBV-BILF1 to determine pharmacological suitability of BILF1 orthologues as model system to study EBV-BILF1 druggability. Cell surface localization, constitutive internalization, and MHC-I downregulation as well as membrane proximal constitutive Gαi signaling patterns were conserved across all BILFs. Only subtle differences between the individual BILFs were observed in downstream transcription factor activation. Using Illumina sequencing, PLHV1 was observed in lymphatic tissue from PTLD-diseased, but not non-diseased pigs. Importantly, these tissues showed enhanced expression of PLHV1-BILF1 supporting its involvement in PTLD infection.
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Affiliation(s)
- Maša Mavri
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valentina Kubale
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Daniel P. Depledge
- Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Jianmin Zuo
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Christene A. Huang
- Department of Surgery, Division of Plastic & Reconstructive Surgery, Division of Transplant Surgery, Anschutz Medical Campus, University of Colorado, Denver, CO, United States
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Milka Vrecl
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michael A. Jarvis
- The Vaccine Group Ltd, Plymouth; and the University of Plymouth, Plymouth, United Kingdom
| | - Eva Jarc Jovičić
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Bernhard Ehlers
- Division 12, Measles, Mumps, Rubella, and Viruses Affecting Immunocompromised Patients, Robert Koch Institute, Berlin, Germany
| | - Mette M. Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Katja Spiess, ; ; Mette M. Rosenkilde,
| | - Katja Spiess
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Katja Spiess, ; ; Mette M. Rosenkilde,
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13
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Braspenning SE, Verjans GMGM, Mehraban T, Messaoudi I, Depledge DP, Ouwendijk WJD. The architecture of the simian varicella virus transcriptome. PLoS Pathog 2021; 17:e1010084. [PMID: 34807956 PMCID: PMC8648126 DOI: 10.1371/journal.ppat.1010084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/06/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Primary infection with varicella-zoster virus (VZV) causes varicella and the establishment of lifelong latency in sensory ganglion neurons. In one-third of infected individuals VZV reactivates from latency to cause herpes zoster, often complicated by difficult-to-treat chronic pain. Experimental infection of non-human primates with simian varicella virus (SVV) recapitulates most features of human VZV disease, thereby providing the opportunity to study the pathogenesis of varicella and herpes zoster in vivo. However, compared to VZV, the transcriptome and the full coding potential of SVV remains incompletely understood. Here, we performed nanopore direct RNA sequencing to annotate the SVV transcriptome in lytically SVV-infected African green monkey (AGM) and rhesus macaque (RM) kidney epithelial cells. We refined structures of canonical SVV transcripts and uncovered numerous RNA isoforms, splicing events, fusion transcripts and non-coding RNAs, mostly unique to SVV. We verified the expression of canonical and newly identified SVV transcripts in vivo, using lung samples from acutely SVV-infected cynomolgus macaques. Expression of selected transcript isoforms, including those located in the unique left-end of the SVV genome, was confirmed by reverse transcription PCR. Finally, we performed detailed characterization of the SVV homologue of the VZV latency-associated transcript (VLT), located antisense to ORF61. Analogous to VZV VLT, SVV VLT is multiply spliced and numerous isoforms are generated using alternative transcription start sites and extensive splicing. Conversely, low level expression of a single spliced SVV VLT isoform defines in vivo latency. Notably, the genomic location of VLT core exons is highly conserved between SVV and VZV. This work thus highlights the complexity of lytic SVV gene expression and provides new insights into the molecular biology underlying lytic and latent SVV infection. The identification of the SVV VLT homolog further underlines the value of the SVV non-human primate model to develop new strategies for prevention of herpes zoster. Varicella-zoster virus (VZV)–a ubiquitous human pathogen–infects most individuals during childhood, leading to chickenpox, after which the virus persists in the host for decades. Later in life, VZV reactivates to cause shingles, frequently associated with difficult-to-treat chronic pain. Our limited understanding of the viral life-cycle hampers the development of more effective treatment options. Simian varicella virus (SVV) is the non-human primate homologue of VZV and causes a natural disease in Old World monkeys with clinical, pathological, and immunological features resembling human VZV infection. However, it is unclear how similar both viruses are at the molecular level. Here, we have revisited the genome-wide transcriptional activity of SVV during lytic infection of kidney epithelial cells derived from two non-human primate species and validated expression of newly identified viral transcripts in lung tissue from SVV-infected animals. Together, this has led to the identification of numerous alternative RNA isoforms, mostly unique to SVV, and some of which may have functional implications for the virus. Notably, we defined the SVV latency-associated transcript, which is highly similar to its VZV counterpart. In conclusion, our study shows the value of understanding the molecular biology of a given animal model and identifies potentially conserved mechanism of latency.
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Affiliation(s)
| | | | - Tamana Mehraban
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
- Institute of Virology, Hannover Medical School, Hannover, Germany
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14
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Braspenning SE, Lebbink RJ, Depledge DP, Schapendonk CME, Anderson LA, Verjans GMGM, Sadaoka T, Ouwendijk WJD. Mutagenesis of the Varicella-Zoster Virus Genome Demonstrates That VLT and VLT-ORF63 Proteins Are Dispensable for Lytic Infection. Viruses 2021; 13:v13112289. [PMID: 34835095 PMCID: PMC8619377 DOI: 10.3390/v13112289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022] Open
Abstract
Primary varicella-zoster virus (VZV) infection leads to varicella and the establishment of lifelong latency in sensory ganglion neurons. Reactivation of latent VZV causes herpes zoster, which is frequently associated with chronic pain. Latent viral gene expression is restricted to the VZV latency-associated transcript (VLT) and VLT-ORF63 (VLT63) fusion transcripts. Since VLT and VLT63 encode proteins that are expressed during lytic infection, we investigated whether pVLT and pVLT-ORF63 are essential for VZV replication by performing VZV genome mutagenesis using CRISPR/Cas9 and BAC technologies. We first established that CRISPR/Cas9 can efficiently mutate VZV genomes in lytically VZV-infected cells through targeting non-essential genes ORF8 and ORF11 and subsequently show recovery of viable mutant viruses. By contrast, the VLT region was markedly resistant to CRISPR/Cas9 editing. Whereas most mutants expressed wild-type or N-terminally altered versions of pVLT and pVLT-ORF63, only a minority of the resulting mutant viruses lacked pVLT and pVLT-ORF63 coding potential. Growth curve analysis showed that pVLT/pVLT-ORF63 negative viruses were viable, but impaired in growth in epithelial cells. We confirmed this phenotype independently using BAC-derived pVLT/pVLT-ORF63 negative and repaired viruses. Collectively, these data demonstrate that pVLT and/or pVLT-ORF63 are dispensable for lytic VZV replication but promote efficient VZV infection in epithelial cells.
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Affiliation(s)
- Shirley E. Braspenning
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (C.M.E.S.); (L.A.A.); (G.M.G.M.V.)
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands;
| | - Daniel P. Depledge
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany;
| | - Claudia M. E. Schapendonk
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (C.M.E.S.); (L.A.A.); (G.M.G.M.V.)
| | - Laura A. Anderson
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (C.M.E.S.); (L.A.A.); (G.M.G.M.V.)
| | - Georges M. G. M. Verjans
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (C.M.E.S.); (L.A.A.); (G.M.G.M.V.)
| | - Tomohiko Sadaoka
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
- Correspondence: (T.S.); (W.J.D.O.); Tel.: +81-78-382-6272 (T.S.); +31-10-7032134 (W.J.D.O.)
| | - Werner J. D. Ouwendijk
- Department of Viroscience, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (C.M.E.S.); (L.A.A.); (G.M.G.M.V.)
- Correspondence: (T.S.); (W.J.D.O.); Tel.: +81-78-382-6272 (T.S.); +31-10-7032134 (W.J.D.O.)
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15
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Gatherer D, Depledge DP, Hartley CA, Szpara ML, Vaz PK, Benkő M, Brandt CR, Bryant NA, Dastjerdi A, Doszpoly A, Gompels UA, Inoue N, Jarosinski KW, Kaul R, Lacoste V, Norberg P, Origgi FC, Orton RJ, Pellett PE, Schmid DS, Spatz SJ, Stewart JP, Trimpert J, Waltzek TB, Davison AJ. ICTV Virus Taxonomy Profile: Herpesviridae 2021. J Gen Virol 2021; 102. [PMID: 34704922 PMCID: PMC8604186 DOI: 10.1099/jgv.0.001673] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the family Herpesviridae have enveloped, spherical virions with characteristic complex structures consisting of symmetrical and non-symmetrical components. The linear, double-stranded DNA genomes of 125–241 kbp contain 70–170 genes, of which 43 have been inherited from an ancestral herpesvirus. In general, herpesviruses have coevolved with and are highly adapted to their hosts, which comprise many mammalian, avian and reptilian species. Following primary infection, they are able to establish lifelong latent infection, during which there is limited viral gene expression. Severe disease is usually observed only in the foetus, the very young, the immunocompromised or following infection of an alternative host. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Herpesviridae, which is available at ictv.global/report/herpesviridae.
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Affiliation(s)
| | | | | | | | - Paola K Vaz
- The University of Melbourne, Victoria, Australia
| | - Mária Benkő
- Veterinary Medical Research Institute, Eötvös Loránd Research Network, Budapest, Hungary
| | | | | | - Akbar Dastjerdi
- Animal and Plant Health Agency-Weybridge, Addlestone, Surrey, UK
| | - Andor Doszpoly
- Veterinary Medical Research Institute, Eötvös Loránd Research Network, Budapest, Hungary
| | - Ursula A Gompels
- Virokine Therapeutics, London BioScience Innovation Centre, Royal Veterinary College, London, UK
| | | | | | - Rajeev Kaul
- University of Delhi South Campus, New Delhi, India
| | | | | | | | | | - Philip E Pellett
- Wayne State University School of Medicine, Detroit, Michigan, USA
| | - D Scott Schmid
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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16
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Depledge DP, Breuer J. Varicella-Zoster Virus-Genetics, Molecular Evolution and Recombination. Curr Top Microbiol Immunol 2021; 438:1-23. [PMID: 34374828 DOI: 10.1007/82_2021_238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This chapter first details the structure, organization and coding content of the VZV genome to provide a foundation on which the molecular evolution of the virus can be projected. We subsequently describe the evolution of molecular profiling approaches from restriction fragment length polymorphisms to single nucleotide polymorphism profiling to modern day high-throughput sequencing approaches. We describe how the application of these methodologies led to our current model of VZV phylogeograpy including the number and structure of geographic clades and the role of recombination in reshaping these.
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Affiliation(s)
- Daniel P Depledge
- Institute of Virology, Hannover Medical School (MHH), Hannover, Germany. .,Department of Microbiology, NYU School of Medicine, New York, USA.
| | - Judith Breuer
- Department of Infection & Immunology, University College London, London, UK
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17
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Srinivas KP, Depledge DP, Abebe JS, Rice SA, Mohr I, Wilson AC. Widespread remodeling of the m 6A RNA-modification landscape by a viral regulator of RNA processing and export. Proc Natl Acad Sci U S A 2021; 118:e2104805118. [PMID: 34282019 PMCID: PMC8325250 DOI: 10.1073/pnas.2104805118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal messenger RNA (mRNA) modification, contributing to the processing, stability, and function of methylated RNAs. Methylation occurs in the nucleus during pre-mRNA synthesis and requires a core methyltransferase complex consisting of METTL3, METTL14, and WTAP. During herpes simplex virus (HSV-1) infection, cellular gene expression is profoundly suppressed, allowing the virus to monopolize the host transcription and translation apparatus and antagonize antiviral responses. The extent to which HSV-1 uses or manipulates the m6A pathway is not known. Here, we show that, in primary fibroblasts, HSV-1 orchestrates a striking redistribution of the nuclear m6A machinery that progresses through the infection cycle. METTL3 and METTL14 are dispersed into the cytoplasm, whereas WTAP remains nuclear. Other regulatory subunits of the methyltransferase complex, along with the nuclear m6A-modified RNA binding protein YTHDC1 and nuclear demethylase ALKBH5, are similarly redistributed. These changes require ICP27, a viral regulator of host mRNA processing that mediates the nucleocytoplasmic export of viral late mRNAs. Viral gene expression is initially reduced by small interfering RNA (siRNA)-mediated inactivation of the m6A methyltransferase but becomes less impacted as the infection advances. Redistribution of the nuclear m6A machinery is accompanied by a wide-scale reduction in the installation of m6A and other RNA modifications on both host and viral mRNAs. These results reveal a far-reaching mechanism by which HSV-1 subverts host gene expression to favor viral replication.
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Affiliation(s)
| | - Daniel P Depledge
- Department of Medicine, New York University Grossman School of Medicine, New York University, New York, NY 10016
| | - Jonathan S Abebe
- Department of Medicine, New York University Grossman School of Medicine, New York University, New York, NY 10016
| | - Stephen A Rice
- Department of Microbiology, University of Minnesota Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Ian Mohr
- Department of Microbiology, New York University Grossman School of Medicine, New York University, New York, NY 10016
| | - Angus C Wilson
- Department of Microbiology, New York University Grossman School of Medicine, New York University, New York, NY 10016;
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18
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Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Targeting the m 6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes Dev 2021; 35:1005-1019. [PMID: 34168039 PMCID: PMC8247602 DOI: 10.1101/gad.348320.121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 11/24/2022]
Abstract
N6-methyladenosine (m6A) is an abundant internal RNA modification, influencing transcript fate and function in uninfected and virus-infected cells. Installation of m6A by the nuclear RNA methyltransferase METTL3 occurs cotranscriptionally; however, the genomes of some cytoplasmic RNA viruses are also m6A-modified. How the cellular m6A modification machinery impacts coronavirus replication, which occurs exclusively in the cytoplasm, is unknown. Here we show that replication of SARS-CoV-2, the agent responsible for the COVID-19 pandemic, and a seasonal human β-coronavirus HCoV-OC43, can be suppressed by depletion of METTL3 or cytoplasmic m6A reader proteins YTHDF1 and YTHDF3 and by a highly specific small molecule METTL3 inhibitor. Reduction of infectious titer correlates with decreased synthesis of viral RNAs and the essential nucleocapsid (N) protein. Sites of m6A modification on genomic and subgenomic RNAs of both viruses were mapped by methylated RNA immunoprecipitation sequencing (meRIP-seq). Levels of host factors involved in m6A installation, removal, and recognition were unchanged by HCoV-OC43 infection; however, nuclear localization of METTL3 and cytoplasmic m6A readers YTHDF1 and YTHDF2 increased. This establishes that coronavirus RNAs are m6A-modified and host m6A pathway components control β-coronavirus replication. Moreover, it illustrates the therapeutic potential of targeting the m6A pathway to restrict coronavirus reproduction.
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Affiliation(s)
- Hannah M Burgess
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, New York 10016, USA
| | - Letitia Thompson
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | | | - Rebecca C Grande
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Elizabeth I Vink
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Jonathan S Abebe
- Department of Medicine, New York University School of Medicine, New York, New York 10016, USA
| | | | - Alan Hendrick
- Storm Therapeutics Ltd, Cambridge CB22 3AT, United Kingdom
| | | | - Tony Kouzarides
- The Gurdon Institute, Department of Pathology, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Kenneth A Stapleford
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
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19
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Dallari S, Heaney T, Rosas-Villegas A, Neil JA, Wong SY, Brown JJ, Urbanek K, Herrmann C, Depledge DP, Dermody TS, Cadwell K. Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome. Cell Host Microbe 2021; 29:1014-1029.e8. [PMID: 33894129 PMCID: PMC8192460 DOI: 10.1016/j.chom.2021.03.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
The contributions of the viral component of the microbiome-the virome-to the development of innate and adaptive immunity are largely unknown. Here, we systematically defined the host response in mice to a panel of eukaryotic enteric viruses representing six different families. Infections with most of these viruses were asymptomatic in the mice, the magnitude and duration of which was dependent on the microbiota. Flow cytometric and transcriptional profiling of mice mono-associated with these viruses unveiled general adaptations by the host, such as lymphocyte differentiation and IL-22 signatures in the intestine, as well as numerous viral-strain-specific responses that persisted. Comparison with a dataset derived from analogous bacterial mono-association in mice identified bacterial species that evoke an immune response comparable with the viruses we examined. These results expand an understanding of the immune space occupied by the enteric virome and underscore the importance of viral exposure events.
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Affiliation(s)
- Simone Dallari
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Thomas Heaney
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Adriana Rosas-Villegas
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Jessica A Neil
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Serre-Yu Wong
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA; Department of Medicine, Henry D. Janowitz Division of Gastroenterology, Susan and Leonard Feinstein Inflammatory Bowel Disease Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy J Brown
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Biology, Trevecca Nazarene University, Nashville, TN, USA
| | - Kelly Urbanek
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christin Herrmann
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniel P Depledge
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Terence S Dermody
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ken Cadwell
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, NY, USA.
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20
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Rüeger S, Hammer C, Loetscher A, McLaren PJ, Lawless D, Naret O, Khanna N, Bernasconi E, Cavassini M, Günthard HF, Kahlert CR, Rauch A, Depledge DP, Morfopoulou S, Breuer J, Zdobnov E, Fellay J. Author Correction: The influence of human genetic variation on Epstein-Barr virus sequence diversity. Sci Rep 2021; 11:8946. [PMID: 33879823 PMCID: PMC8058043 DOI: 10.1038/s41598-021-87274-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Sina Rüeger
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Alexis Loetscher
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Dylan Lawless
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Naret
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nina Khanna
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
- Childrens Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, UK
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Evgeny Zdobnov
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jacques Fellay
- School of Life Sciences, EPFL, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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21
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Rüeger S, Hammer C, Loetscher A, McLaren PJ, Lawless D, Naret O, Khanna N, Bernasconi E, Cavassini M, Günthard HF, Kahlert CR, Rauch A, Depledge DP, Morfopoulou S, Breuer J, Zdobnov E, Fellay J. The influence of human genetic variation on Epstein-Barr virus sequence diversity. Sci Rep 2021; 11:4586. [PMID: 33633271 PMCID: PMC7907281 DOI: 10.1038/s41598-021-84070-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Epstein-Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imprint of host genomic variation on the EBV sequence, we jointly analyzed paired viral and human genomic data from 268 HIV-coinfected individuals with CD4 + T cell count < 200/mm3 and elevated EBV viremia. We hypothesized that the reactivated virus circulating in these patients could carry sequence variants acquired during primary EBV infection, thereby providing a snapshot of early adaptation to the pressure exerted on EBV by the individual immune response. We searched for associations between host and pathogen genetic variants, taking into account human and EBV population structure. Our analyses revealed significant associations between human and EBV sequence variation. Three polymorphic regions in the human genome were found to be associated with EBV variation: one at the amino acid level (BRLF1:p.Lys316Glu); and two at the gene level (burden testing of rare variants in BALF5 and BBRF1). Our findings confirm that jointly analyzing host and pathogen genomes can identify sites of genomic interactions, which could help dissect pathogenic mechanisms and suggest new therapeutic avenues.
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Affiliation(s)
- Sina Rüeger
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Alexis Loetscher
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Dylan Lawless
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Naret
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nina Khanna
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
- Childrens Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, UK
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Evgeny Zdobnov
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jacques Fellay
- School of Life Sciences, EPFL, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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22
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Ouwendijk WJD, Depledge DP, Rajbhandari L, Lenac Rovis T, Jonjic S, Breuer J, Venkatesan A, Verjans GMGM, Sadaoka T. Varicella-zoster virus VLT-ORF63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency. Nat Commun 2020; 11:6324. [PMID: 33303747 PMCID: PMC7730162 DOI: 10.1038/s41467-020-20031-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Varicella-zoster virus (VZV) establishes lifelong neuronal latency in most humans world-wide, reactivating in one-third to cause herpes zoster and occasionally chronic pain. How VZV establishes, maintains and reactivates from latency is largely unknown. VZV transcription during latency is restricted to the latency-associated transcript (VLT) and RNA 63 (encoding ORF63) in naturally VZV-infected human trigeminal ganglia (TG). While significantly more abundant, VLT levels positively correlated with RNA 63 suggesting co-regulated transcription during latency. Here, we identify VLT-ORF63 fusion transcripts and confirm VLT-ORF63, but not RNA 63, expression in human TG neurons. During in vitro latency, VLT is transcribed, whereas VLT-ORF63 expression is induced by reactivation stimuli. One isoform of VLT-ORF63, encoding a fusion protein combining VLT and ORF63 proteins, induces broad viral gene transcription. Collectively, our findings show that VZV expresses a unique set of VLT-ORF63 transcripts, potentially involved in the transition from latency to lytic VZV infection.
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Affiliation(s)
- Werner J D Ouwendijk
- Department of Viroscience, Erasmus Medical Centre, 3015 CN, Rotterdam, The Netherlands
| | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Labchan Rajbhandari
- Division of Neuroimmunology and Neuroinfectious Diseases, Department of Neurology, Johns Hopkins University School of Medicine, 600 N. Wolfe St., Meyer 6-113, Baltimore, MD, 21287, USA
| | - Tihana Lenac Rovis
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, 51000, Croatia
| | - Stipan Jonjic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, 51000, Croatia
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Arun Venkatesan
- Division of Neuroimmunology and Neuroinfectious Diseases, Department of Neurology, Johns Hopkins University School of Medicine, 600 N. Wolfe St., Meyer 6-113, Baltimore, MD, 21287, USA
| | - Georges M G M Verjans
- Department of Viroscience, Erasmus Medical Centre, 3015 CN, Rotterdam, The Netherlands
| | - Tomohiko Sadaoka
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
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23
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Price AM, Hayer KE, McIntyre ABR, Gokhale NS, Abebe JS, Della Fera AN, Mason CE, Horner SM, Wilson AC, Depledge DP, Weitzman MD. Direct RNA sequencing reveals m 6A modifications on adenovirus RNA are necessary for efficient splicing. Nat Commun 2020; 11:6016. [PMID: 33243990 PMCID: PMC7691994 DOI: 10.1038/s41467-020-19787-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022] Open
Abstract
Adenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral RNAs have been previously detected, the location and function of this mark within the infectious cycle is unknown. Since the complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, here we profile m6A within the adenovirus transcriptome using a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transcript-resolved m6A detection. Although both early and late viral transcripts contain m6A, depletion of m6A writer METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution, and highlight the role of m6A in regulating splicing of a viral pathogen.
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Affiliation(s)
- Alexander M Price
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alexa B R McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, 10065, USA
- Department of Molecular Life Sciences, University of Zurich, 8006, Zurich, Switzerland
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Immunology, University of Washington, Seattle, WA, 98115, USA
| | - Jonathan S Abebe
- Department of Medicine, New York University School of Medicine, New York, NY, 10017, USA
| | - Ashley N Della Fera
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Biological Sciences Graduate Group, University of Maryland, College Park, MD, 20742, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- The World Quant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, 10017, USA
| | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, NY, 10017, USA.
| | - Matthew D Weitzman
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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24
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Braspenning SE, Sadaoka T, Breuer J, Verjans GMGM, Ouwendijk WJD, Depledge DP. Decoding the Architecture of the Varicella-Zoster Virus Transcriptome. mBio 2020; 11:e01568-20. [PMID: 33024035 PMCID: PMC7542360 DOI: 10.1128/mbio.01568-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Varicella-zoster virus (VZV), a double-stranded DNA virus, causes varicella, establishes lifelong latency in ganglionic neurons, and reactivates later in life to cause herpes zoster, commonly associated with chronic pain. The VZV genome is densely packed and produces multitudes of overlapping transcripts deriving from both strands. While 71 distinct open reading frames (ORFs) have thus far been experimentally defined, the full coding potential of VZV remains unknown. Here, we integrated multiple short-read RNA sequencing approaches with long-read direct RNA sequencing on RNA isolated from VZV-infected cells to provide a comprehensive reannotation of the lytic VZV transcriptome architecture. Through precise mapping of transcription start sites, splice junctions, and polyadenylation sites, we identified 136 distinct polyadenylated VZV RNAs that encode canonical ORFs, noncanonical ORFs, and ORF fusions, as well as putative noncoding RNAs (ncRNAs). Furthermore, we determined the kinetic class of all VZV transcripts and observed, unexpectedly, that transcripts encoding the ORF62 protein, previously designated Immediate-Early, were expressed with Late kinetics. Our work showcases the complexity of the VZV transcriptome and provides a comprehensive resource that will facilitate future functional studies of coding RNAs, ncRNAs, and the biological mechanisms underlying the regulation of viral transcription and translation during lytic VZV infection.IMPORTANCE Transcription from herpesviral genomes, executed by the host RNA polymerase II and regulated by viral proteins, results in coordinated viral gene expression to efficiently produce infectious progeny. However, the complete coding potential and regulation of viral gene expression remain ill-defined for the human alphaherpesvirus varicella-zoster virus (VZV), causative agent of both varicella and herpes zoster. Here, we present a comprehensive overview of the VZV transcriptome and the kinetic class of all identified viral transcripts, using two virus strains and two biologically relevant cell types. Additionally, our data provide an overview of how VZV diversifies its transcription from one of the smallest herpesviral genomes. Unexpectedly, the transcript encoding the major viral transactivator protein (pORF62) was expressed with Late kinetics, whereas orthologous transcripts in other alphaherpesviruses are typically expressed during the immediate early phase. Therefore, our work both establishes the architecture of the VZV transcriptome and provides insight into regulation of alphaherpesvirus gene expression.
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Affiliation(s)
| | - Tomohiko Sadaoka
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Judith Breuer
- Department of Infection and Immunity, University College London, London, United Kingdom
| | | | | | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, New York, USA
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25
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Abstract
The genomes of DNA viruses encode deceptively complex transcriptomes evolved to maximize coding potential within the confines of a relatively small genome. Defining the full range of viral RNAs produced during an infection is key to understanding the viral replication cycle and its interactions with the host cell. Traditional short-read (Illumina) sequencing approaches are problematic in this setting due to the difficulty of assigning short reads to individual RNAs in regions of transcript overlap and to the biases introduced by the required recoding and amplification steps. Additionally, different methodologies may be required to analyze the 5' and 3' ends of RNAs, which increases both cost and effort. The advent of long-read nanopore sequencing simplifies this approach by providing a single assay that captures and sequences full length RNAs, either in cDNA or native RNA form. The latter is particularly appealing as it reduces known recoding biases whilst allowing more advanced analyses such as estimation of poly(A) tail length and the detection of RNA modifications including N6 -methyladenosine. Using herpes simplex virus (HSV)-infected primary fibroblasts as a template, we provide a step-by-step guide to the production of direct RNA sequencing libraries suitable for sequencing using Oxford Nanopore Technologies platforms and provide a simple computational approach to deriving a high-quality annotation of the HSV transcriptome from the resulting sequencing data. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Productive infection of primary fibroblasts with herpes simplex virus Support Protocol: Cell passage and plating of primary fibroblasts Basic Protocol 2: Preparation and sequencing of dRNA-seq libraries from virus-infected cells Basic Protocol 3: Processing, alignment, and analysis of dRNA-seq datasets.
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Affiliation(s)
- Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, New York
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, New York
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26
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Jensen NJ, Depledge DP, Ng TFF, Leung J, Quinlivan M, Radford KW, Folster J, Tseng HF, LaRussa P, Jacobsen SJ, Breuer J, Schmid DS. Analysis of the reiteration regions (R1 to R5) of varicella-zoster virus. Virology 2020; 546:38-50. [PMID: 32452416 DOI: 10.1016/j.virol.2020.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/12/2020] [Accepted: 03/31/2020] [Indexed: 10/24/2022]
Abstract
The varicella-zoster virus (VZV) genome, comprises both unique and repeated regions. The genome also includes reiteration regions, designated R1 to R5, which are tandemly repeating sequences termed elements. These regions represent an understudied feature of the VZV genome. The R4 region is duplicated, with one copy in the internal repeat short (IRs) which we designated R4A and a second copy in the terminal repeat short (TRs) termed R4B. We developed primers to amplify and Sanger sequence these regions, including independent amplification of both R4 regions. Reiteration regions from >80 cases of PCR-confirmed shingles were sequenced and analyzed. Complete genome sequences for the remaining portions of these viruses were determined using Illumina MiSeq. We identified 28 elements not previously reported, including at least one element for each R region. Length heterogeneity was substantial in R3, R4A and R4B. Length heterogeneity between the two copies of R4 was common.
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Affiliation(s)
- Nancy J Jensen
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, United Kingdom; Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Terry Fei Fan Ng
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica Leung
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark Quinlivan
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kay W Radford
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer Folster
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hung-Fu Tseng
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Philip LaRussa
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Steven J Jacobsen
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - D Scott Schmid
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Harbecke R, Jensen NJ, Depledge DP, Johnson GR, Ashbaugh ME, Schmid DS, Breuer J, Levin MJ, Oxman MN. Recurrent herpes zoster in the Shingles Prevention Study: Are second episodes caused by the same varicella-zoster virus strain? Vaccine 2020; 38:150-157. [PMID: 31679866 DOI: 10.1016/j.vaccine.2019.10.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/01/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022]
Abstract
Herpes zoster (HZ) is caused by reactivation of varicella zoster virus (VZV) that established latency in sensory and autonomic neurons during primary infection. In the Shingles Prevention Study (SPS), a large efficacy trial of live attenuated Oka/Merck zoster vaccine (ZVL), PCR-confirmed second episodes of HZ occurred in two of 660 placebo and one of 321 ZVL recipients with documented HZ during a mean follow-up of 3.13 years. An additional two ZVL recipients experienced a second episode of HZ in the Long-Term Persistence Substudy. All episodes of HZ were caused by wild-type VZV. The first and second episodes of HZ occurred in different dermatomes in each of these five participants, with contralateral recurrences in two. Time between first and second episodes ranged from 12 to 28 months. One of the five participants, who was immunocompetent on study enrollment, was immunocompromised at the onset of his first and second episodes of HZ. VZV DNA isolated from rash lesions from the first and second episodes of HZ was used to sequence the full-length VZV genomes. For the unique-sequence regions of the VZV genome, we employed target enrichment of VZV DNA, followed by deep sequencing. For the reiteration regions, we used PCR amplification and Sanger sequencing. Our analysis and comparison of the VZV genomes from the first and second episodes of HZ in each of the five participants indicate that both episodes were caused by the same VZV strain. This is consistent with the extraordinary stability of VZV during the replication phase of varicella and the subsequent establishment of latency in sensory ganglia throughout the body. Our observations also indicate that VZV is stable during the persistence of latency and the subsequent reactivation and replication that results in HZ.
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Affiliation(s)
- Ruth Harbecke
- Department of Veterans Affairs (VA) San Diego Healthcare System, San Diego, CA, USA; Department of Medicine, University of California San Diego, San Diego, CA, USA.
| | - Nancy J Jensen
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, USA
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, UK; Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Gary R Johnson
- Cooperative Studies Program Coordinating Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Mark E Ashbaugh
- Department of Veterans Affairs (VA) San Diego Healthcare System, San Diego, CA, USA
| | - D Scott Schmid
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, USA
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Myron J Levin
- Department of Medicine and Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Michael N Oxman
- Department of Veterans Affairs (VA) San Diego Healthcare System, San Diego, CA, USA; Department of Medicine, University of California San Diego, San Diego, CA, USA
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28
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Lassalle F, Beale MA, Bharucha T, Williams CA, Williams RJ, Cudini J, Goldstein R, Haque T, Depledge DP, Breuer J. Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses. Virus Evol 2020; 6:veaa012. [PMID: 32099667 PMCID: PMC7031915 DOI: 10.1093/ve/veaa012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Herpes Simplex Virus type 1 (HSV-1) chronically infects over 70 per cent of the global population. Clinical manifestations are largely restricted to recurrent epidermal vesicles. However, HSV-1 also leads to encephalitis, the infection of the brain parenchyma, with high associated rates of mortality and morbidity. In this study, we performed target enrichment followed by direct sequencing of HSV-1 genomes, using target enrichment methods on the cerebrospinal fluid (CSF) of clinical encephalitis patients and from skin swabs of epidermal vesicles on non-encephalopathic patients. Phylogenetic analysis revealed high inter-host diversity and little population structure. In contrast, samples from different lesions in the same patient clustered with similar patterns of allelic variants. Comparison of consensus genome sequences shows HSV-1 has been freely recombining, except for distinct islands of linkage disequilibrium (LD). This suggests functional constraints prevent recombination between certain genes, notably those encoding pairs of interacting proteins. Distinct LD patterns characterised subsets of viruses recovered from CSF and skin lesions, which may reflect different evolutionary constraints in different body compartments. Functions of genes under differential constraint related to immunity or tropism and provide new hypotheses on tissue-specific mechanisms of viral infection and latency.
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Affiliation(s)
- Florent Lassalle
- Department of Infectious Disease Epidemiology, Imperial College London, St-Mary's Hospital campus, Praed Street, London W2 1NY, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, St-Mary's Hospital campus, Praed Street, London W2 1NY, UK
| | - Mathew A Beale
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Tehmina Bharucha
- Department of Virology, Royal Free Hospital, 10 Pond Street, Hampstead, London NW3 2PS, UK
| | - Charlotte A Williams
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Rachel J Williams
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Juliana Cudini
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Richard Goldstein
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Tanzina Haque
- Department of Virology, Royal Free Hospital, 10 Pond Street, Hampstead, London NW3 2PS, UK
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH
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29
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Tommasi C, Rogerson C, Depledge DP, Jones M, Naeem AS, Venturini C, Frampton D, Tutill HJ, Way B, Breuer J, O'Shaughnessy RFL. Kallikrein-Mediated Cytokeratin 10 Degradation Is Required for Varicella Zoster Virus Propagation in Skin. J Invest Dermatol 2019; 140:774-784.e11. [PMID: 31626786 DOI: 10.1016/j.jid.2019.08.448] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 11/30/2022]
Abstract
Varicella zoster virus (VZV) is a skin-tropic virus that infects epidermal keratinocytes and causes chickenpox. Although common, VZV infection can be life-threatening, particularly in the immunocompromized. Therefore, understanding VZV-keratinocyte interactions is important to find new treatments beyond vaccination and antiviral drugs. In VZV-infected skin, kallikrein 6 and the ubiquitin ligase MDM2 are upregulated concomitant with keratin 10 (KRT10) downregulation. MDM2 binds to KRT10, targeting it for degradation via the ubiquitin-proteasome pathway. Preventing KRT10 degradation reduced VZV propagation in culture and prevented epidermal disruption in skin explants. KRT10 knockdown induced expression of NR4A1 and enhanced viral propagation in culture. NR4A1 knockdown prevented viral propagation in culture, reduced LC3 levels, and increased LAMP2 expression. We therefore describe a drug-able pathway whereby MDM2 ubiquitinates and degrades KRT10, increasing NR4A1 expression and allowing VZV replication and propagation.
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Affiliation(s)
- Cristina Tommasi
- Livingstone Skin Research Centre, Immunobiology and Dermatology, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Clare Rogerson
- Centre for Cell Biology and Cutaneous Research, Queen Mary University of London, London, United Kingdom
| | - Daniel P Depledge
- Infection and Immunity, University College London, London, United Kingdom; Department of Microbiology, New York University, New York, New York
| | - Meleri Jones
- Centre for Cell Biology and Cutaneous Research, Queen Mary University of London, London, United Kingdom; Infection and Immunity, University College London, London, United Kingdom
| | - Aishath S Naeem
- Livingstone Skin Research Centre, Immunobiology and Dermatology, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Cristina Venturini
- Infection and Immunity, University College London, London, United Kingdom
| | - Dan Frampton
- Infection and Immunity, University College London, London, United Kingdom
| | - Helena J Tutill
- Infection and Immunity, University College London, London, United Kingdom
| | - Benjamin Way
- Livingstone Skin Research Centre, Immunobiology and Dermatology, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Judith Breuer
- Infection and Immunity, University College London, London, United Kingdom
| | - Ryan F L O'Shaughnessy
- Livingstone Skin Research Centre, Immunobiology and Dermatology, University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Centre for Cell Biology and Cutaneous Research, Queen Mary University of London, London, United Kingdom.
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30
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Depledge DP, Cudini J, Kundu S, Atkinson C, Brown JR, Haque T, Houldcroft CJ, Koay ES, McGill F, Milne R, Whitfield T, Tang JW, Underhill G, Bergstrom T, Norberg P, Goldstein R, Solomon T, Breuer J. High Viral Diversity and Mixed Infections in Cerebral Spinal Fluid From Cases of Varicella Zoster Virus Encephalitis. J Infect Dis 2019; 218:1592-1601. [PMID: 29986093 PMCID: PMC6173578 DOI: 10.1093/infdis/jiy358] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 06/28/2018] [Indexed: 11/13/2022] Open
Abstract
Background Varicella zoster virus (VZV) may cause encephalitis, both with and without rash. Here we investigate whether viruses recovered from the central nervous system (CNS; encephalitis or meningitis) differ genetically from those recovered from non-CNS samples. Methods Enrichment-based deep sequencing of 45 VZV genomes from cerebral spinal fluid (CSF), plasma, bronchoalveolar lavage (BAL), and vesicles was carried out with samples collected from 34 patients with and without VZV infection of the CNS. Results Viral sequences from multiple sites in the same patient were identical at the consensus level. Virus from vesicle fluid and CSF in cases of meningitis showed low-level diversity. By contrast, plasma, BAL, and encephalitis had higher numbers of variant alleles. Two CSF-encephalitis samples had high genetic diversity, with variant frequency patterns typical of mixed infections with different clades. Conclusions Low viral genetic diversity in vesicle fluid is compatible with previous observations that VZV skin lesions arise from single or low numbers of virions. A similar result was observed in VZV from cases of VZV meningitis, a generally self-limiting infection. CSF from cases of encephalitis had higher diversity with evidence for mixed clade infections in 2 cases. We hypothesize that reactivation from multiple neurons may contribute to the pathogenesis of VZV encephalitis.
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Affiliation(s)
| | - Juliana Cudini
- Division of Infection and Immunity, University College London
| | - Samit Kundu
- School of Human and Life Sciences, Canterbury Christ Church University, University of Kent
| | | | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital NHS Foundation Trust, London
| | | | | | - Evelyn S Koay
- Department of Pathology, National University of Singapore.,Department of Infectious Diseases, Section for Clinical Virology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Fiona McGill
- Institute of Infection and Global Health, University of Liverpool.,National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool.,Royal Liverpool University Hospitals
| | - Richard Milne
- Division of Infection and Immunity, University College London
| | - Tom Whitfield
- Institute of Infection and Global Health, University of Liverpool
| | - Julian W Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust.,Molecular Diagnosis Centre, National University Hospital, Singapore
| | - Gillian Underhill
- Departments of Clinical Microbiology, Pathology Centre, Queen Alexandra Hospital, Portsmouth
| | - Tomas Bergstrom
- Department of Infectious Diseases, Section for Clinical Virology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Peter Norberg
- Department of Infectious Diseases, Section for Clinical Virology, Institute of Biomedicine, University of Gothenburg, Sweden
| | | | - Tom Solomon
- Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London
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31
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Wegner F, Lassalle F, Depledge DP, Balloux F, Breuer J. Co-evolution of sites under immune selection shapes Epstein-Barr Virus population structure. Mol Biol Evol 2019; 36:2512-2521. [PMID: 31273385 PMCID: PMC6805225 DOI: 10.1093/molbev/msz152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 06/03/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Epstein–Barr virus (EBV) is one of the most common viral infections in humans and persists within its host for life. EBV therefore represents an extremely successful virus that has evolved complex strategies to evade the host’s innate and adaptive immune response during both initial and persistent stages of infection. Here, we conducted a comparative genomics analysis on 223 whole genome sequences of worldwide EBV strains. We recover extensive genome-wide linkage disequilibrium (LD) despite pervasive genetic recombination. This pattern is explained by the global EBV population being subdivided into three main subpopulations, one primarily found in East Asia, one in Southeast Asia and Oceania, and the third including most of the other globally distributed genomes we analyzed. Additionally, sites in LD were overrepresented in immunogenic genes. Taken together, our results suggest that host immune selection and local adaptation to different human host populations has shaped the genome-wide patterns of genetic diversity in EBV.
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Affiliation(s)
- Fanny Wegner
- Division of Infection & Immunity, University College London, London, UK.,Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
| | - Florent Lassalle
- UCL Genetic Institute, University College London, London, UK.,MRC Centre for Outbreak Analysis and Modelling, Imperial College, London, UK
| | - Daniel P Depledge
- Division of Infection & Immunity, University College London, London, UK
| | | | - Judith Breuer
- Division of Infection & Immunity, University College London, London, UK
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32
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Depledge DP, Srinivas KP, Sadaoka T, Bready D, Mori Y, Placantonakis DG, Mohr I, Wilson AC. Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen. Nat Commun 2019; 10:754. [PMID: 30765700 PMCID: PMC6376126 DOI: 10.1038/s41467-019-08734-9] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
Characterizing complex viral transcriptomes by conventional RNA sequencing approaches is complicated by high gene density, overlapping reading frames, and complex splicing patterns. Direct RNA sequencing (direct RNA-seq) using nanopore arrays offers an exciting alternative whereby individual polyadenylated RNAs are sequenced directly, without the recoding and amplification biases inherent to other sequencing methodologies. Here we use direct RNA-seq to profile the herpes simplex virus type 1 (HSV-1) transcriptome during productive infection of primary cells. We show how direct RNA-seq data can be used to define transcription initiation and RNA cleavage sites associated with all polyadenylated viral RNAs and demonstrate that low level read-through transcription produces a novel class of chimeric HSV-1 transcripts, including a functional mRNA encoding a fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L. Thus, direct RNA-seq offers a powerful method to characterize the changing transcriptional landscape of viruses with complex genomes.
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Affiliation(s)
- Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA.
| | | | - Tomohiko Sadaoka
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Devin Bready
- Department of Neurosurgery, New York University School of Medicine, New York, NY, 10016, USA
| | - Yasuko Mori
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Dimitris G Placantonakis
- Department of Neurosurgery, New York University School of Medicine, New York, NY, 10016, USA
- Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
- Brain Tumor Center, New York University School of Medicine, New York, NY, 10016, USA
- Neuroscience Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA.
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
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33
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Depledge DP, Mohr I, Wilson AC. Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes. J Virol 2019; 93:e01342-18. [PMID: 30305358 PMCID: PMC6288342 DOI: 10.1128/jvi.01342-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022] Open
Abstract
Transcriptome profiling has become routine in studies of many biological processes. However, the favored approaches such as short-read Illumina RNA sequencing are giving way to long-read sequencing platforms better suited to interrogating the complex transcriptomes typical of many RNA and DNA viruses. Here, we provide a guide-tailored to molecular virologists-to the ins and outs of viral transcriptome sequencing and discuss the strengths and weaknesses of the major RNA sequencing technologies as tools to analyze the abundance and diversity of the viral transcripts made during infection.
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Affiliation(s)
- Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
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34
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Rubio RM, Depledge DP, Bianco C, Thompson L, Mohr I. RNA m 6 A modification enzymes shape innate responses to DNA by regulating interferon β. Genes Dev 2018; 32:1472-1484. [PMID: 30463905 PMCID: PMC6295168 DOI: 10.1101/gad.319475.118] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/12/2018] [Indexed: 12/21/2022]
Abstract
In this study, Rubio et al. researched how the dynamic genome-wide landscape of m6A-modified mRNAs impacts virus infection and host immune responses. They show that type I interferon (IFN) production triggered by dsDNA or human cytomegalovirus (HCMV) is controlled by the cellular m6A methyltrasferase subunit METTL14 and ALKBH5 demethylase, and their results demonstrate that responses to nonmicrobial dsDNA in uninfected cells are regulated by enzymes controlling m6A epitranscriptomic changes. Modification of mRNA by N6-adenosine methylation (m6A) on internal bases influences gene expression in eukaryotes. How the dynamic genome-wide landscape of m6A-modified mRNAs impacts virus infection and host immune responses remains poorly understood. Here, we show that type I interferon (IFN) production triggered by dsDNA or human cytomegalovirus (HCMV) is controlled by the cellular m6A methyltrasferase subunit METTL14 and ALKBH5 demethylase. While METTL14 depletion reduced virus reproduction and stimulated dsDNA- or HCMV-induced IFNB1 mRNA accumulation, ALKBH5 depletion had the opposite effect. Depleting METTL14 increased both nascent IFNB1 mRNA production and stability in response to dsDNA. In contrast, ALKBH5 depletion reduced nascent IFNB1 mRNA production without detectably influencing IFN1B mRNA decay. Genome-wide transcriptome profiling following ALKBH5 depletion identified differentially expressed genes regulating antiviral immune responses, while METTL14 depletion altered pathways impacting metabolic reprogramming, stress responses, and aging. Finally, we determined that IFNB1 mRNA was m6A-modified within both the coding sequence and the 3′ untranslated region (UTR). This establishes that the host m6A modification machinery controls IFNβ production triggered by HCMV or dsDNA. Moreover, it demonstrates that responses to nonmicrobial dsDNA in uninfected cells, which shape host immunity and contribute to autoimmune disease, are regulated by enzymes controlling m6A epitranscriptomic changes.
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Affiliation(s)
- Rosa M Rubio
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Christopher Bianco
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Letitia Thompson
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA.,Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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35
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Abstract
Meeting Report on the 8th Annual Symposium of the Colorado Alphaherpesvirus Latency Society (CALS), held on May 16-19, 2018, in Vail, Colorado.
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Affiliation(s)
- Nicholas L Baird
- Department of Neurology, University of Colorado School of Medicine, 12700 E. 19th Ave, Mail Stop B1182, Aurora, CO, 80045, USA
| | - Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
| | - Randall J Cohrs
- Department of Neurology, University of Colorado School of Medicine, 12700 E. 19th Ave, Mail Stop B1182, Aurora, CO, 80045, USA. .,Department of Immunology and Microbiology, University of Colorado School of Medicine, 12700 E. 19th Avenue, Mail Stop B182, Aurora, CO, 80045, USA.
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36
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Houldcroft CJ, Roy S, Morfopoulou S, Margetts BK, Depledge DP, Cudini J, Shah D, Brown JR, Romero EY, Williams R, Cloutman-Green E, Rao K, Standing JF, Hartley JC, Breuer J. Use of Whole-Genome Sequencing of Adenovirus in Immunocompromised Pediatric Patients to Identify Nosocomial Transmission and Mixed-Genotype Infection. J Infect Dis 2018; 218:1261-1271. [PMID: 29917114 DOI: 10.1093/infdis/jiy323] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/26/2018] [Indexed: 01/26/2023] Open
Abstract
Background Adenoviruses are significant pathogens for the immunocompromised, arising from primary infection or reinfection. Serotyping is insufficient to support nosocomial transmission investigations. We investigate whether whole-genome sequencing (WGS) provides clinically relevant information on transmission among patients in a pediatric tertiary hospital. Methods We developed a target-enriched adenovirus WGS technique for clinical samples and retrospectively sequenced 107 adenovirus-positive residual diagnostic samples, including viremias (>5 × 104 copies/mL), from 37 patients collected January 2011-March 2016. Whole-genome sequencing was used to determine genotype and for phylogenetic analysis. Results Adenovirus sequences were recovered from 105 of 107 samples. Full genome sequences were recovered from all 20 nonspecies C samples and from 36 of 85 species C viruses, with partial genome sequences recovered from the rest. Whole-genome phylogenetic analysis suggested linkage of 3 genotype A31 cases and uncovered an unsuspected epidemiological link to an A31 infection first detected on the same ward 4 years earlier. In 9 samples from 1 patient who died, we identified a mixed genotype adenovirus infection. Conclusions Adenovirus WGS from clinical samples is possible and useful for genotyping and molecular epidemiology. Whole-genome sequencing identified likely nosocomial transmission with greater resolution than conventional genotyping and distinguished between adenovirus disease due to single or multiple genotypes.
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Affiliation(s)
- Charlotte J Houldcroft
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom.,Division of Infection and Immunity, University College London, United Kingdom
| | - Sunando Roy
- Division of Infection and Immunity, University College London, United Kingdom
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, United Kingdom
| | - Ben K Margetts
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom.,Centre for Computation, Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Daniel P Depledge
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom
| | - Juliana Cudini
- Division of Infection and Immunity, University College London, United Kingdom
| | - Divya Shah
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Julianne R Brown
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Erika Yara Romero
- Division of Infection and Immunity, University College London, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, United Kingdom
| | - Elaine Cloutman-Green
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Kanchan Rao
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Joseph F Standing
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - John C Hartley
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Judith Breuer
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom.,Division of Infection and Immunity, University College London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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37
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Heath G, Depledge DP, Brown JR, Hale AD, Tutil H, Williams R, Breuer J. Acute Retinal Necrosis Caused by the Zoster Vaccine Virus. Clin Infect Dis 2018; 65:2122-2125. [PMID: 29020238 PMCID: PMC5849943 DOI: 10.1093/cid/cix683] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/04/2017] [Indexed: 12/14/2022] Open
Abstract
We report acute retinal necrosis caused by the vaccine Oka strain following immunization of a 78-year-old woman with live zoster vaccine. Whole genome sequencing confirmed the ocular vOka strain to be derived from the vaccine and excluded the presence of new mutations or recombination with wild-type Varicella zoster virus.
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Affiliation(s)
- Gregory Heath
- Medical Ophthalmology, York Teaching Hospital NHS Foundation Trust, York, England
| | | | - Julianne R Brown
- Microbiology, Virology and Infection Control (VZV Typing Laboratory), Great Ormond St Hospital, London, England
| | - Anthony D Hale
- Virology, Leeds Teaching Hospitals NHS Trust, Leeds, England
| | - Helena Tutil
- Infection and Immunity, University College London, England
| | | | - Judith Breuer
- Infection and Immunity, University College London, England.,Microbiology, Virology and Infection Control (VZV Typing Laboratory), Great Ormond St Hospital, London, England
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38
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Depledge DP, Sadaoka T, Ouwendijk WJD. Molecular Aspects of Varicella-Zoster Virus Latency. Viruses 2018; 10:v10070349. [PMID: 29958408 PMCID: PMC6070824 DOI: 10.3390/v10070349] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/19/2018] [Accepted: 06/27/2018] [Indexed: 02/07/2023] Open
Abstract
Primary varicella-zoster virus (VZV) infection causes varicella (chickenpox) and the establishment of a lifelong latent infection in ganglionic neurons. VZV reactivates in about one-third of infected individuals to cause herpes zoster, often accompanied by neurological complications. The restricted host range of VZV and, until recently, a lack of suitable in vitro models have seriously hampered molecular studies of VZV latency. Nevertheless, recent technological advances facilitated a series of exciting studies that resulted in the discovery of a VZV latency-associated transcript (VLT) and provide novel insights into our understanding of VZV latency and factors that may initiate reactivation. Deducing the function(s) of VLT and the molecular mechanisms involved should now be considered a priority to improve our understanding of factors that govern VZV latency and reactivation. In this review, we summarize the implications of recent discoveries in the VZV latency field from both a virus and host perspective and provide a roadmap for future studies.
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Affiliation(s)
- Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA.
| | - Tomohiko Sadaoka
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Werner J D Ouwendijk
- Department of Viroscience, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands.
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Greninger AL, Knudsen GM, Roychoudhury P, Hanson DJ, Sedlak RH, Xie H, Guan J, Nguyen T, Peddu V, Boeckh M, Huang ML, Cook L, Depledge DP, Zerr DM, Koelle DM, Gantt S, Yoshikawa T, Caserta M, Hill JA, Jerome KR. Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6. BMC Genomics 2018; 19:204. [PMID: 29554870 PMCID: PMC5859498 DOI: 10.1186/s12864-018-4604-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/13/2018] [Indexed: 12/19/2022] Open
Abstract
Background Human herpesvirus-6A and -6B (HHV-6) are betaherpesviruses that reach > 90% seroprevalence in the adult population. Unique among human herpesviruses, HHV-6 can integrate into the subtelomeric regions of human chromosomes; when this occurs in germ line cells it causes a condition called inherited chromosomally integrated HHV-6 (iciHHV-6). Only two complete genomes are available for replicating HHV-6B, leading to numerous conflicting annotations and little known about the global genomic diversity of this ubiquitous virus. Results Using a custom capture panel for HHV-6B, we report complete genomes from 61 isolates of HHV-6B from active infections (20 from Japan, 35 from New York state, and 6 from Uganda), and 64 strains of iciHHV-6B (mostly from North America). HHV-6B sequence clustered by geography and illustrated extensive recombination. Multiple iciHHV-6B sequences from unrelated individuals across the United States were found to be completely identical, consistent with a founder effect. Several iciHHV-6B strains clustered with strains from recent active pediatric infection. Combining our genomic analysis with the first RNA-Seq and shotgun proteomics studies of HHV-6B, we completely reannotated the HHV-6B genome, altering annotations for more than 10% of existing genes, with multiple instances of novel splicing and genes that hitherto had gone unannotated. Conclusion Our results are consistent with a model of intermittent de novo integration of HHV-6B into host germline cells during active infection with a large contribution of founder effect in iciHHV-6B. Our data provide a significant advance in the genomic annotation of HHV-6B, which will contribute to the detection, diversity, and control of this virus. Electronic supplementary material The online version of this article (10.1186/s12864-018-4604-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA. .,, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.,, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Derek J Hanson
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Ruth Hall Sedlak
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Jon Guan
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Thuy Nguyen
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Vikas Peddu
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Michael Boeckh
- , Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Linda Cook
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, UK
| | - Danielle M Zerr
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - David M Koelle
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Soren Gantt
- University of British Columbia, BC Children's Hospital Research Institute, Vancouver, Canada
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University, Fujita, Toyoake, Japan
| | - Mary Caserta
- University of Rochester Medical Center School of Medicine, Rochester, New York, USA
| | - Joshua A Hill
- , Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.,, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Depledge DP, Brown J, Macanovic J, Underhill G, Breuer J. Viral Genome Sequencing Proves Nosocomial Transmission of Fatal Varicella. J Infect Dis 2016; 214:1399-1402. [PMID: 27571904 PMCID: PMC5079377 DOI: 10.1093/infdis/jiw398] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/22/2016] [Indexed: 12/05/2022] Open
Abstract
We report the first use of whole viral genome sequencing to identify nosocomial transmission of varicella-zoster virus with fatal outcome. The index case patient, nursed in source isolation, developed disseminated zoster with rash present for 1 day before being transferred to the intensive care unit (ICU). Two patients who had received renal transplants while inpatients in an adjacent ward developed chickenpox and 1 died; neither patient had direct contact with the index patient.
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Affiliation(s)
| | - Julianne Brown
- Great Ormond Street Hospital VZV Reference Laboratory, Great Ormond Street Hospital, London
| | | | - Gill Underhill
- Departments of Clinical Microbiology, Pathology Centre, Queen Alexandra Hospital, Cosham, Portsmouth, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London
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Houldcroft CJ, Bryant JM, Depledge DP, Margetts BK, Simmonds J, Nicolaou S, Tutill HJ, Williams R, Worth AJJ, Marks SD, Veys P, Whittaker E, Breuer J. Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus. Front Microbiol 2016; 7:1317. [PMID: 27667983 PMCID: PMC5016526 DOI: 10.3389/fmicb.2016.01317] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/09/2016] [Indexed: 11/13/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a significant pathogen in immunocompromised individuals, with the potential to cause fatal pneumonitis and colitis, as well as increasing the risk of organ rejection in transplant patients. With the advent of new anti-HCMV drugs there is therefore considerable interest in using virus sequence data to monitor emerging resistance to antiviral drugs in HCMV viraemia and disease, including the identification of putative new mutations. We used target-enrichment to deep sequence HCMV DNA from 11 immunosuppressed pediatric patients receiving single or combination anti-HCMV treatment, serially sampled over 1–27 weeks. Changes in consensus sequence and resistance mutations were analyzed for three ORFs targeted by anti-HCMV drugs and the frequencies of drug resistance mutations monitored. Targeted-enriched sequencing of clinical material detected mutations occurring at frequencies of 2%. Seven patients showed no evidence of drug resistance mutations. Four patients developed drug resistance mutations a mean of 16 weeks after starting treatment. In two patients, multiple resistance mutations accumulated at frequencies of 20% or less, including putative maribavir and ganciclovir resistance mutations P522Q (UL54) and C480F (UL97). In one patient, resistance was detected 14 days earlier than by PCR. Phylogenetic analysis suggested recombination or superinfection in one patient. Deep sequencing of HCMV enriched from clinical samples excluded resistance in 7 of 11 subjects and identified resistance mutations earlier than conventional PCR-based resistance testing in 2 patients. Detection of multiple low level resistance mutations was associated with poor outcome.
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Affiliation(s)
- Charlotte J Houldcroft
- Infection, Immunity, Inflammation and Physiological Medicine, Institute of Child Health, University College LondonLondon, UK; Division of Infection and Immunity, University College LondonLondon, UK
| | - Josephine M Bryant
- Division of Infection and Immunity, University College London London, UK
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London London, UK
| | - Ben K Margetts
- Infection, Immunity, Inflammation and Physiological Medicine, Institute of Child Health, University College LondonLondon, UK; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College LondonLondon, UK
| | - Jacob Simmonds
- Great Ormond Street Hospital for Children NHS Foundation Trust London, UK
| | - Stephanos Nicolaou
- Division of Infection and Immunity, University College London London, UK
| | - Helena J Tutill
- Division of Infection and Immunity, University College London London, UK
| | - Rachel Williams
- Division of Infection and Immunity, University College London London, UK
| | - Austen J J Worth
- Great Ormond Street Hospital for Children NHS Foundation Trust London, UK
| | - Stephen D Marks
- Infection, Immunity, Inflammation and Physiological Medicine, Institute of Child Health, University College LondonLondon, UK; Great Ormond Street Hospital for Children NHS Foundation TrustLondon, UK
| | - Paul Veys
- Great Ormond Street Hospital for Children NHS Foundation Trust London, UK
| | | | - Judith Breuer
- Infection, Immunity, Inflammation and Physiological Medicine, Institute of Child Health, University College LondonLondon, UK; Division of Infection and Immunity, University College LondonLondon, UK; Great Ormond Street Hospital for Children NHS Foundation TrustLondon, UK
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42
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Sadaoka T, Depledge DP, Rajbhandari L, Venkatesan A, Breuer J, Cohen JI. In vitro system using human neurons demonstrates that varicella-zoster vaccine virus is impaired for reactivation, but not latency. Proc Natl Acad Sci U S A 2016; 113:E2403-12. [PMID: 27078099 PMCID: PMC4855584 DOI: 10.1073/pnas.1522575113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Varicella-zoster virus (VZV) establishes latency in human sensory and cranial nerve ganglia during primary infection (varicella), and the virus can reactivate and cause zoster after primary infection. The mechanism of how the virus establishes and maintains latency and how it reactivates is poorly understood, largely due to the lack of robust models. We found that axonal infection of neurons derived from hESCs in a microfluidic device with cell-free parental Oka (POka) VZV resulted in latent infection with inability to detect several viral mRNAs by reverse transcriptase-quantitative PCR, no production of infectious virus, and maintenance of the viral DNA genome in endless configuration, consistent with an episome configuration. With deep sequencing, however, multiple viral mRNAs were detected. Treatment of the latently infected neurons with Ab to NGF resulted in production of infectious virus in about 25% of the latently infected cultures. Axonal infection of neurons with vaccine Oka (VOka) VZV resulted in a latent infection similar to infection with POka; however, in contrast to POka, VOka-infected neurons were markedly impaired for reactivation after treatment with Ab to NGF. In addition, viral transcription was markedly reduced in neurons latently infected with VOka compared with POka. Our in vitro system recapitulates both VZV latency and reactivation in vivo and may be used to study viral vaccines for their ability to establish latency and reactivate.
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Affiliation(s)
- Tomohiko Sadaoka
- Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Daniel P Depledge
- Division of Infection and Immunity, MRC Centre for Medical Molecular Virology, University College London, London WC1E 6BT, United Kingdom
| | - Labchan Rajbhandari
- Division of Neuroimmunology and Neuroinfectious Diseases, Department of Neurology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, MD 21287
| | - Arun Venkatesan
- Division of Neuroimmunology and Neuroinfectious Diseases, Department of Neurology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, MD 21287
| | - Judith Breuer
- Division of Infection and Immunity, MRC Centre for Medical Molecular Virology, University College London, London WC1E 6BT, United Kingdom
| | - Jeffrey I Cohen
- Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
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43
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Lassalle F, Depledge DP, Reeves MB, Brown AC, Christiansen MT, Tutill HJ, Williams RJ, Einer-Jensen K, Holdstock J, Atkinson C, Brown JR, van Loenen FB, Clark DA, Griffiths PD, Verjans GM, Schutten M, Milne RS, Balloux F, Breuer J. Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes. Virus Evol 2016; 2:vew017. [PMID: 30288299 PMCID: PMC6167919 DOI: 10.1093/ve/vew017] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout the host's life in a latent state with periodic episodes of reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by the emergence of antiviral resistance and the absence of an effective vaccine, the development of which is likely complicated by the numerous immune evasins encoded by HCMV to counter the host's adaptive immune responses, a feature that facilitates frequent super-infections. Understanding the evolutionary dynamics of HCMV is essential for the development of effective new drugs and vaccines. By comparing viral genomes from uncultivated or low-passaged clinical samples of diverse origins, we observe evidence of frequent homologous recombination events, both recent and ancient, and no structure of HCMV genetic diversity at the whole-genome scale. Analysis of individual gene-scale loci reveals a striking dichotomy: while most of the genome is highly conserved, recombines essentially freely and has evolved under purifying selection, 21 genes display extreme diversity, structured into distinct genotypes that do not recombine with each other. Most of these hyper-variable genes encode glycoproteins involved in cell entry or escape of host immunity. Evidence that half of them have diverged through episodes of intense positive selection suggests that rapid evolution of hyper-variable loci is likely driven by interactions with host immunity. It appears that this process is enabled by recombination unlinking hyper-variable loci from strongly constrained neighboring sites. It is conceivable that viral mechanisms facilitating super-infection have evolved to promote recombination between diverged genotypes, allowing the virus to continuously diversify at key loci to escape immune detection, while maintaining a genome optimally adapted to its asymptomatic infectious lifecycle.
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Affiliation(s)
- Florent Lassalle
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Daniel P. Depledge
- Division of Infection and Immunity, University College London, London, United
Kingdom
| | - Matthew B. Reeves
- Division of Infection and Immunity, University College London, London, United
Kingdom
| | | | - Mette T. Christiansen
- Division of Infection and Immunity, University College London, London, United
Kingdom
| | - Helena J. Tutill
- Division of Infection and Immunity, University College London, London, United
Kingdom
| | - Rachel J. Williams
- Division of Infection and Immunity, University College London, London, United
Kingdom
| | | | | | - Claire Atkinson
- Department of Virology, Royal Free Hospital, London, United Kingdom
| | - Julianne R. Brown
- Microbiology, Virology and Infection Prevention and Control, Camelia Botnar
Laboratories, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United
Kingdom
| | | | - Duncan A. Clark
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
| | - Paul D. Griffiths
- Division of Infection and Immunity, University College London, London, United
Kingdom
| | | | - Martin Schutten
- Department of Viroscience, Erasmus, MC Rotterdam, the Netherlands
| | - Richard S.B. Milne
- Division of Infection and Immunity, University College London, London, United
Kingdom
| | - Francois Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United
Kingdom
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Weinert LA, Depledge DP, Kundu S, Gershon AA, Nichols RA, Balloux F, Welch JJ, Breuer J. Rates of vaccine evolution show strong effects of latency: implications for varicella zoster virus epidemiology. Mol Biol Evol 2015; 32:1020-8. [PMID: 25568346 PMCID: PMC4379407 DOI: 10.1093/molbev/msu406] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Varicella-zoster virus (VZV) causes chickenpox and shingles, and is found in human populations worldwide. The lack of temporal signal in the diversity of VZV makes substitution rate estimates unreliable, which is a barrier to understanding the context of its global spread. Here, we estimate rates of evolution by studying live attenuated vaccines, which evolved in 22 vaccinated patients for known periods of time, sometimes, but not always undergoing latency. We show that the attenuated virus evolves rapidly (∼ 10(-6) substitutions/site/day), but that rates decrease dramatically when the virus undergoes latency. These data are best explained by a model in which viral populations evolve for around 13 days before becoming latent, but then undergo no replication during latency. This implies that rates of viral evolution will depend strongly on transmission patterns. Nevertheless, we show that implausibly long latency periods are required to date the most recent common ancestor of extant VZV to an "out-of-Africa" migration with humans, as has been previously suggested.
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Affiliation(s)
- Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom Department of Genetics, Evolution and Environment, UCL, London, United Kingdom
| | - Daniel P Depledge
- Division of Infection and Immunity, MRC Centre for Medical Molecular Virology, UCL, London, United Kingdom
| | - Samit Kundu
- Division of Infection and Immunity, MRC Centre for Medical Molecular Virology, UCL, London, United Kingdom
| | - Anne A Gershon
- Division of Infectious Disease, Columbia University Medical Centre, New York, USA
| | - Richard A Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Francois Balloux
- Department of Genetics, Evolution and Environment, UCL, London, United Kingdom
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, MRC Centre for Medical Molecular Virology, UCL, London, United Kingdom
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Christiansen MT, Brown AC, Kundu S, Tutill HJ, Williams R, Brown JR, Holdstock J, Holland MJ, Stevenson S, Dave J, Tong CYW, Einer-Jensen K, Depledge DP, Breuer J. Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples. BMC Infect Dis 2014; 14:591. [PMID: 25388670 PMCID: PMC4233057 DOI: 10.1186/s12879-014-0591-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/27/2014] [Indexed: 12/30/2022] Open
Abstract
Background Chlamydia trachomatis is a pathogen of worldwide importance, causing more than 100 million cases of sexually transmitted infections annually. Whole-genome sequencing is a powerful high resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The objective of this study was to perform whole-genome enrichment and sequencing of C. trachomatis directly from clinical samples. Methods C. trachomatis positive samples comprising seven vaginal swabs and three urine samples were sequenced without prior in vitro culture in addition to nine cultured C. trachomatis samples, representing different serovars. A custom capture RNA bait set, that captures all known diversity amongst C. trachomatis genomes, was used in a whole-genome enrichment step during library preparation to enrich for C. trachomatis DNA. All samples were sequenced on the MiSeq platform. Results Full length C. trachomatis genomes (>95-100% coverage of a reference genome) were successfully generated for eight of ten clinical samples and for all cultured samples. The proportion of reads mapping to C. trachomatis and the mean read depth across each genome were strongly linked to the number of bacterial copies within the original sample. Phylogenetic analysis confirmed the known population structure and the data showed potential for identification of minority variants and mutations associated with antimicrobial resistance. The sensitivity of the method was >10-fold higher than other reported methodologies. Conclusions The combination of whole-genome enrichment and deep sequencing has proven to be a non-mutagenic approach, capturing all known variation found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0591-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mette T Christiansen
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| | - Amanda C Brown
- Oxford Gene Technology, Begbroke, Oxfordshire, OX5 1PF, UK. .,Present address: Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA.
| | - Samit Kundu
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK. .,School of Human and Life Sciences, Canterbury Christchurch University, Canterbury, Kent, CT1 1QU, UK.
| | - Helena J Tutill
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| | - Rachel Williams
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| | | | | | - Martin J Holland
- London School of Hygiene and Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
| | - Simon Stevenson
- University College London Hospital (UCLH), London, WC1E 6DE, UK.
| | | | | | | | - Daniel P Depledge
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| | - Judith Breuer
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
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Depledge DP, Kundu S, Jensen NJ, Gray ER, Jones M, Steinberg S, Gershon A, Kinchington PR, Schmid DS, Balloux F, Nichols RA, Breuer J. Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans. Mol Biol Evol 2013; 31:397-409. [PMID: 24162921 PMCID: PMC3907055 DOI: 10.1093/molbev/mst210] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Immunization with the vOka vaccine prevents varicella (chickenpox) in children and susceptible adults. The vOka vaccine strain comprises a mixture of genotypes and, despite attenuation, causes rashes in small numbers of recipients. Like wild-type virus, the vaccine establishes latency in neuronal tissue and can later reactivate to cause Herpes zoster (shingles). Using hybridization-based methodologies, we have purified and sequenced vOka directly from skin lesions. We show that alleles present in the vaccine can be recovered from the lesions and demonstrate the presence of a severe bottleneck between inoculation and lesion formation. Genotypes in any one lesion appear to be descended from one to three vaccine-genotypes with a low frequency of novel mutations. No single vOka haplotype and no novel mutations are consistently present in rashes, indicating that neither new mutations nor recombination with wild type are critical to the evolution of vOka rashes. Instead, alleles arising from attenuation (i.e., not derived from free-living virus) are present at lower frequencies in rash genotypes. We identify 11 loci at which the ancestral allele is selected for in vOka rash formation and show genotypes in rashes that have reactivated from latency cannot be distinguished from rashes occurring immediately after inoculation. We conclude that the vOka vaccine, although heterogeneous, has not evolved to form rashes through positive selection in the mode of a quasispecies, but rather alleles that were essentially neutral during the vaccine production have been selected against in the human subjects, allowing us to identify key loci for rash formation.
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Affiliation(s)
- Daniel P Depledge
- MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, London, United Kingdom
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47
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Kundu S, Lockwood J, Depledge DP, Chaudhry Y, Aston A, Rao K, Hartley JC, Goodfellow I, Breuer J. Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients. Clin Infect Dis 2013; 57:407-14. [PMID: 23645848 DOI: 10.1093/cid/cit287] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Noroviruses are a highly transmissible and major cause of nosocomial gastroenteritis resulting in bed and hospital-ward closures. Where hospital outbreaks are suspected, it is important to determine the routes of spread so that appropriate infection-control procedures can be implemented. To investigate a cluster of norovirus cases occurring in children undergoing bone marrow transplant, we undertook norovirus genome sequencing by next-generation methods. Detailed comparison of sequence data from 2 linked cases enabled us to identify the likely direction of spread. METHODS Norovirus complementary DNA was amplified by overlapping polymerase chain reaction (PCR) from 13 stool samples from 5 diagnostic real-time PCR-positive patients. The amplicons were sequenced by Roche 454, the genomes assembled by de novo assembly, and the data analyzed phylogenetically. RESULTS Phylogenetic analysis indicated that patients were infected by viruses similar to 4 distinct GII.4 subtypes and 2 patients were linked by the same virus. Of the 14 sites at which there were differences between the consensus sequences of the 2 linked viral genomes, 9 had minor variants present within one or the other patient. Further analysis confirmed that minor variants at all 9 sites in patient B w ere present as the consensus sequence in patient A. CONCLUSIONS Phylogenetic analysis excluded a common source of infection in this apparent outbreak. Two of 3 patients on the same ward had closely related viruses, raising the possibility of cross-infection despite protective isolation. Analysis of deep sequencing data enabled us to establish the likely direction of nosocomial transmission.
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Affiliation(s)
- Samit Kundu
- Division of Infection and Immunity, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom.
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48
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Watson SJ, Welkers MRA, Depledge DP, Coulter E, Breuer JM, de Jong MD, Kellam P. Viral population analysis and minority-variant detection using short read next-generation sequencing. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120205. [PMID: 23382427 PMCID: PMC3678329 DOI: 10.1098/rstb.2012.0205] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
RNA viruses within infected individuals exist as a population of evolutionary-related variants. Owing to evolutionary change affecting the constitution of this population, the frequency and/or occurrence of individual viral variants can show marked or subtle fluctuations. Since the development of massively parallel sequencing platforms, such viral populations can now be investigated to unprecedented resolution. A critical problem with such analyses is the presence of sequencing-related errors that obscure the identification of true biological variants present at low frequency. Here, we report the development and assessment of the Quality Assessment of Short Read (QUASR) Pipeline (http://sourceforge.net/projects/quasr) specific for virus genome short read analysis that minimizes sequencing errors from multiple deep-sequencing platforms, and enables post-mapping analysis of the minority variants within the viral population. QUASR significantly reduces the error-related noise in deep-sequencing datasets, resulting in increased mapping accuracy and reduction of erroneous mutations. Using QUASR, we have determined influenza virus genome dynamics in sequential samples from an in vitro evolution of 2009 pandemic H1N1 (A/H1N1/09) influenza from samples sequenced on both the Roche 454 GSFLX and Illumina GAIIx platforms. Importantly, concordance between the 454 and Illumina sequencing allowed unambiguous minority-variant detection and accurate determination of virus population turnover in vitro.
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Affiliation(s)
- Simon J Watson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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49
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Depledge DP, Palser AL, Watson SJ, Lai IYC, Gray ER, Grant P, Kanda RK, Leproust E, Kellam P, Breuer J. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One 2011; 6:e27805. [PMID: 22125625 PMCID: PMC3220689 DOI: 10.1371/journal.pone.0027805] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 10/25/2011] [Indexed: 11/29/2022] Open
Abstract
Whole genome sequencing of viruses directly from clinical samples is integral for understanding the genetics of host-virus interactions. Here, we report the use of sample sparing target enrichment (by hybridisation) for viral nucleic acid separation and deep-sequencing of herpesvirus genomes directly from a range of clinical samples including saliva, blood, virus vesicles, cerebrospinal fluid, and tumour cell lines. We demonstrate the effectiveness of the method by deep-sequencing 13 highly cell-associated human herpesvirus genomes and generating full length genome alignments at high read depth. Moreover, we show the specificity of the method enables the study of viral population structures and their diversity within a range of clinical samples types.
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Affiliation(s)
- Daniel P Depledge
- Division of Infection and Immunity, University College London, London, United Kingdom.
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50
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Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates PA, Depledge DP, Harris D, Her Y, Herzyk P, Imamura H, Otto TD, Sanders M, Seeger K, Dujardin JC, Berriman M, Smith DF, Hertz-Fowler C, Mottram JC. Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res 2011; 21:2129-42. [PMID: 22038252 DOI: 10.1101/gr.122945.111] [Citation(s) in RCA: 316] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Leishmania parasites cause a spectrum of clinical pathology in humans ranging from disfiguring cutaneous lesions to fatal visceral leishmaniasis. We have generated a reference genome for Leishmania mexicana and refined the reference genomes for Leishmania major, Leishmania infantum, and Leishmania braziliensis. This has allowed the identification of a remarkably low number of genes or paralog groups (2, 14, 19, and 67, respectively) unique to one species. These were found to be conserved in additional isolates of the same species. We have predicted allelic variation and find that in these isolates, L. major and L. infantum have a surprisingly low number of predicted heterozygous SNPs compared with L. braziliensis and L. mexicana. We used short read coverage to infer ploidy and gene copy numbers, identifying large copy number variations between species, with 200 tandem gene arrays in L. major and 132 in L. mexicana. Chromosome copy number also varied significantly between species, with nine supernumerary chromosomes in L. infantum, four in L. mexicana, two in L. braziliensis, and one in L. major. A significant bias against gene arrays on supernumerary chromosomes was shown to exist, indicating that duplication events occur more frequently on disomic chromosomes. Taken together, our data demonstrate that there is little variation in unique gene content across Leishmania species, but large-scale genetic heterogeneity can result through gene amplification on disomic chromosomes and variation in chromosome number. Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression in response to environmental conditions in the host, providing a genetic basis for disease tropism.
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Affiliation(s)
- Matthew B Rogers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
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