1
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Kim TY, Park MS, Yun SA, Kang M, Kim DR, Shin A, Kim HY, Jang MA, Jang JH, Kwon MJ, Huh HJ, Kim YJ, Lee NY. Performance evaluation of the SMG HHV-6 Q Real-Time PCR Kit for quantitative detection and differentiation of human herpesvirus 6A and 6B. Microbiol Spectr 2024; 12:e0424923. [PMID: 38451228 PMCID: PMC10986541 DOI: 10.1128/spectrum.04249-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
The aim of this study was to compare the performance of the newly developed SMG HHV-6 Q Real-Time PCR Kit (SMG assay) with the RealStar HHV-6 PCR Kit (RealStar assay). The analytical sensitivity and specificity, linearity, and precision of the SMG assay were evaluated. The clinical performance of the SMG assay was assessed and compared with that of the RealStar assay using 207 clinical specimens (HHV-6A positive, n = 51; HHV-6B positive, n = 64; HHV-6A/B negative, n = 92). The limit of detection of the SMG assay was 2.92 log10 copies/mL for HHV-6A DNA and 2.88 log10 copies/mL for HHV-6B DNA. The linear range was determined to be 3.40-9.00 log10 copies/mL for both viruses. Intra- and inter-assay variability were below 5% at concentrations ranging from 4 to 9 log10 copies/mL. No cross-reactivity was observed with the 25 microorganisms included in the specificity panel. The clinical sensitivity and specificity of the SMG and RealStar assays compared to in-house polymerase chain reaction and sequencing were as follows: SMG assay, 98.0% and 100% for HHV-6A DNA, respectively, and 96.9% and 100% for HHV-6B DNA, respectively; RealStar assay, 98.0% and 100% for HHV-6A DNA, respectively, and 90.6% and 100% for HHV-6B DNA, respectively. The correlation coefficients between viral loads measured by the two assays were 0.948 and 0.975, with mean differences of 0.62 and 0.32 log10 copies/mL for HHV-6A and HHV-6B DNA, respectively. These results demonstrate that the SMG assay is a sensitive and reliable tool for the quantitative detection and differentiation of HHV-6A and HHV-6B DNA.IMPORTANCEQuantitative real-time PCR (qPCR) that can distinguish between HHV-6A and HHV-6B DNA is recommended for diagnosis of active infection. The SMG HHV-6 Q Real-Time PCR Kit (SMG assay) is a newly developed qPCR assay that can differentiate between HHV-6A and HHV-6B DNA; however, little is known about its performance. In this study, we assessed the performance of the SMG assay and compared it with that of a commercially available qPCR assay, the RealStar HHV-6 PCR Kit (RealStar assay). The SMG assay demonstrated excellent analytical sensitivity and specificity, precision, and linearity. Furthermore, the viral loads measured by the SMG assay were highly correlated with those measured by the RealStar assay. Our results suggest that the SMG assay is a useful diagnostic tool for quantitative detection and differentiation of HHV-6A and HHV-6B DNA.
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Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Min-Seung Park
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, South Korea
| | - Minhee Kang
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Doo Ri Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Areum Shin
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hyun-Young Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Min-Jung Kwon
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Yae-Jean Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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2
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Gompels UA, Bravo FJ, Briggs S, Ameri S, Cardin RD, Bernstein DI. Immunisation Using Novel DNA Vaccine Encoding Virus Membrane Fusion Complex and Chemokine Genes Shows High Protection from HSV-2. Viruses 2022; 14:v14112317. [PMID: 36366414 PMCID: PMC9698128 DOI: 10.3390/v14112317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2022] Open
Abstract
Herpes simplex virus 1 and 2 infections cause high unmet disease burdens worldwide. Mainly HSV-2 causes persistent sexually transmitted disease, fatal neonatal disease and increased transmission of HIV/AIDS. Thus, there is an urgent requirement to develop effective vaccines. We developed nucleic acid vaccines encoding a novel virus entry complex stabilising cell membrane fusion, 'virus-like membranes', VLM. Two dose intramuscular immunisations using DNA expression plasmids in a guinea pig model gave 100% protection against acute disease and significantly reduced virus replication after virus intravaginal challenge. There was also reduced establishment of latency within the dorsal root ganglia and spinal cord, but recurrent disease and recurrent virus shedding remained. To increase cellular immunity and protect against recurrent disease, cDNA encoding an inhibitor of chemokine receptors on T regulatory cells was added and compared to chemokine CCL5 effects. Immunisation including this novel human chemokine gene, newly defined splice variant from an endogenous virus genome, 'virokine immune therapeutic', VIT, protected most guinea pigs from recurrent disease and reduced recurrent virus shedding distinct from a gD protein vaccine similar to that previously evaluated in clinical trials. All DNA vaccines induced significant neutralising antibodies and warrant evaluation for new therapeutic treatments.
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Affiliation(s)
- Ursula A. Gompels
- Virothera, Milner Therapeutics Institute, Cambridge Biomedical Campus, Cambridge CB4 0WS, UK
- Correspondence:
| | - Fernando J. Bravo
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Sean Briggs
- Virothera, Milner Therapeutics Institute, Cambridge Biomedical Campus, Cambridge CB4 0WS, UK
| | - Shima Ameri
- Virothera, Milner Therapeutics Institute, Cambridge Biomedical Campus, Cambridge CB4 0WS, UK
| | - Rhonda D. Cardin
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - David I. Bernstein
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45221, USA
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3
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Collin V, Flamand L. [The importance of telomeres in human herpesvirus-6A/B infections]. Med Sci (Paris) 2022; 38:168-176. [PMID: 35179471 DOI: 10.1051/medsci/2022008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Herpesviruses are undisputed masters of disguise. The ability to become invisible to the immune system effectors is a complex process resting on a variety of stealth approaches. Among these, human herpesviruses-6A and -6B (HHV-6A/B) have developed the unique ability to integrate their genome within the ends of chromosomes allowing viral persistence in the absence of viral protein expression. This aptitude, unique to HHV-6A/B among human herpesviruses, requires close interactions between the telomeric regions of chromosomes and the viral genome. In this review article, the biology of telomeres and the mechanisms responsible for viral integration are discussed. In closing, the possible biological consequences of HHV-6A/B integration into chromosomal DNA are discussed.
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Affiliation(s)
- Vanessa Collin
- Axe des maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec - Université Laval, Québec, 2705 boulevard Laurier, Québec, Canada
| | - Louis Flamand
- Axe des maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec - Université Laval, Québec, 2705 boulevard Laurier, Québec, Canada - Département de microbiologie, maladies infectieuses et immunologie, Faculté de médecine, Université Laval, Québec, 2705 boulevard Laurier, Québec, Canada
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4
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Mouammine A, Gravel A, Dubuc I, Feroz Zada Y, Provost S, Busseuil D, Tardif JC, Dubé MP, Flamand L. rs73185306 C/T Is Not a Predisposing Risk Factor for Inherited Chromosomally Integrated Human Herpesvirus 6A/B. J Infect Dis 2020; 221:878-881. [PMID: 31621866 DOI: 10.1093/infdis/jiz527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/10/2019] [Indexed: 01/18/2023] Open
Abstract
Approximately 1% of people worldwide carry a copy of the human herpesvirus 6A or 6B (HHV-6A/B) in every cell of their body. This condition is referred to as inherited chromosomally integrated HHV-6A/B (iciHHV-6A/B). The mechanisms leading to iciHHV-6A/B chromosomal integration are yet to be identified. A recent report suggested that the rs73185306 C/T single-nucleotide polymorphism (SNP) represents a favorable predisposing factor leading to HHV-6A/B integration. After genotype analysis of an independent cohort (N = 11 967), we report no association between the rs73185306 C/T SNP and HHV-6A/B chromosomal integration (odds ratio, 0.90 [95% confidence interval, .54-1.51]; P = .69).
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Affiliation(s)
- Annabelle Mouammine
- Division of Infectious and Immune Diseases, Centre Hospitalier Universitaire de Quebec Research Center, Laval University, Quebec City, Quebec, Canada
| | - Annie Gravel
- Division of Infectious and Immune Diseases, Centre Hospitalier Universitaire de Quebec Research Center, Laval University, Quebec City, Quebec, Canada
| | - Isabelle Dubuc
- Division of Infectious and Immune Diseases, Centre Hospitalier Universitaire de Quebec Research Center, Laval University, Quebec City, Quebec, Canada
| | | | | | | | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, Canada.,Faculty of Medicine, Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montreal, Quebec, Canada.,Faculty of Medicine, Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Louis Flamand
- Division of Infectious and Immune Diseases, Centre Hospitalier Universitaire de Quebec Research Center, Laval University, Quebec City, Quebec, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
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5
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Santpere G, Telford M, Andrés-Benito P, Navarro A, Ferrer I. The Presence of Human Herpesvirus 6 in the Brain in Health and Disease. Biomolecules 2020; 10:E1520. [PMID: 33172107 PMCID: PMC7694807 DOI: 10.3390/biom10111520] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/03/2023] Open
Abstract
The human herpesvirus 6 (HHV-6) -A and -B are two dsDNA beta-herpesviruses infectingalmost the entire worldwide population. These viruses have been implicated in multipleneurological conditions in individuals of various ages and immunological status, includingencephalitis, epilepsy, and febrile seizures. HHV-6s have also been suggested as playing a role inthe etiology of neurodegenerative diseases such as multiple sclerosis and Alzheimer's disease. Theapparent robustness of these suggested associations is contingent on the accuracy of HHV-6detection in the nervous system. The effort of more than three decades of researching HHV-6 in thebrain has yielded numerous observations, albeit using variable technical approaches in terms oftissue preservation, detection techniques, sample sizes, brain regions, and comorbidities. In thisreview, we aimed to summarize current knowledge about the entry routes and direct presence ofHHV-6 in the brain parenchyma at the level of DNA, RNA, proteins, and specific cell types, inhealthy subjects and in those with neurological conditions. We also discuss recent findings relatedto the presence of HHV-6 in the brains of patients with Alzheimer's disease in light of availableevidence.
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Affiliation(s)
- Gabriel Santpere
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), DCEXS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Marco Telford
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, 08003 Barcelona, Catalonia, Spain; (M.T.); (A.N.)
| | - Pol Andrés-Benito
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain;
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, 08003 Barcelona, Catalonia, Spain; (M.T.); (A.N.)
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Wellington 30, 08005 Barcelona, Spain
| | - Isidre Ferrer
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain;
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, 08907 Barcelona, Spain
- Bellvitge University Hospital, IDIBELL (Bellvitge Biomedical Research Centre), Hospitalet de Llobregat, 08908 Barcelona, Spain
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6
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Lathe R, St Clair D. From conifers to cognition: Microbes, brain and behavior. GENES BRAIN AND BEHAVIOR 2020; 19:e12680. [PMID: 32515128 DOI: 10.1111/gbb.12680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/12/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022]
Abstract
A diversity of bacteria, protozoans and viruses ("endozoites") were recently uncovered within healthy tissues including the human brain. By contrast, it was already recognized a century ago that healthy plants tissues contain abundant endogenous microbes ("endophytes"). Taking endophytes as an informative precedent, we overview the nature, prevalence, and role of endozoites in mammalian tissues, centrally focusing on the brain, concluding that endozoites are ubiquitous in diverse tissues. These passengers often remain subclinical, but they are not silent. We address their routes of entry, mechanisms of persistence, tissue specificity, and potential to cause long-term behavioral changes and/or immunosuppression in mammals, where rabies virus is the exemplar. We extend the discussion to Herpesviridae, Coronaviridae, and Toxoplasma, as well as to diverse bacteria and yeasts, and debate the advantages and disadvantages that endozoite infection might afford to the host and to the ecosystem. We provide a clinical perspective in which endozoites are implicated in neurodegenerative disease, anxiety/depression, and schizophrenia. We conclude that endozoites are instrumental in the delicate balance between health and disease, including age-related brain disease, and that endozoites have played an important role in the evolution of brain function and human behavior.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh Medical School, Edinburgh, UK
| | - David St Clair
- Institute of Medical Sciences, School of Medicine, University of Aberdeen, Aberdeen, UK
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7
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Forni D, Cagliani R, Clerici M, Pozzoli U, Sironi M. Evolutionary analysis of exogenous and integrated HHV-6A/HHV-6B populations. Virus Evol 2020; 6:veaa035. [PMID: 32551136 PMCID: PMC7293831 DOI: 10.1093/ve/veaa035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human betaherpesviruses 6A and 6B (HHV-6A and HHV-6B) are highly prevalent in human populations. The genomes of these viruses can be stably integrated at the telomeres of human chromosomes and be vertically transmitted (inherited chromosomally integrated HHV-6A/HHV-6B, iciHHV-6A/iciHHV-6B). We reconstructed the population structures of HHV-6A and HHV-6B, showing that HHV-6A diverged less than HHV-6B genomes from the projected common ancestral population. Thus, HHV-6B genomes experienced stronger drift, as also supported by calculation of nucleotide diversity and Tajima's D. Analysis of ancestry proportions indicated that HHV-6A exogenous viruses and iciHHV-6A derived most of their genomes from distinct ancestral sources. Conversely, ancestry proportions were similar in exogenous HHV-6B viruses and iciHHV-6B. In line with previous indications, this suggests the distinct exogenous viral populations that originated iciHHV-6B in subjects with European and Asian ancestry are still causing infections in the corresponding geographic areas. Notably, for both iciHHV-6A and iciHHV-6B, we found that European and American sequences tend to have high proportions of ancestry from viral populations that experienced considerable drift, suggesting that they underwent one or more bottlenecks followed by population expansion. Finally, analysis of HHV-6B exogenous viruses sampled in Japan indicated that proportions of ancestry components of most of these viruses are different from the majority of those sampled in the USA. More generally, we show that, in both viral species, both integrated and exogenous viral genomes have different ancestry components, partially depending on geographic location. It would be extremely important to determine whether such differences account for the diversity of HHV-6A/HHV-6B-associated clinical symptoms and epidemiology. Also, the sequencing of additional exogenous and integrated viral genomes will be instrumental to confirm and expand our conclusions, which are based on a relatively small number of genomes, sequenced with variable quality, and with unequal sampling in terms of geographic origin.
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Affiliation(s)
- Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20090 Milan, Italy.,IRCCS Fondazione Don Carlo Gnocchi, 20148 Milan, Italy
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
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8
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Arbustini E, Narula N, Giuliani L, Di Toro A. Genetic Basis of Myocarditis: Myth or Reality? MYOCARDITIS 2020. [PMCID: PMC7122345 DOI: 10.1007/978-3-030-35276-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The genetic basis of myocarditis remains an intriguing concept, at least as long as the definition of myocarditis constitutes the definitive presence of myocardial inflammation sufficient to cause the observed ventricular dysfunction in the setting of cardiotropic infections. Autoimmune or immune-mediated myocardial inflammation constitutes a complex area of clinical interest, wherein numerous and not yet fully understood role of hereditary auto-inflammatory diseases can result in inflammation of the pericardium and myocardium. Finally, myocardial involvement in hereditary immunodeficiency diseases, cellular and humoral, is a possible trigger for infections which may complicate the diseases themselves. Whether the role of constitutional genetics can make the patient susceptible to myocardial inflammation remains yet to be explored.
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9
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Houldcroft CJ. Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion. Pathogens 2019; 8:E186. [PMID: 31614759 PMCID: PMC6963362 DOI: 10.3390/pathogens8040186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022] Open
Abstract
The nine human herpesviruses are some of the most ubiquitous pathogens worldwide, causing life-long latent infection in a variety of different tissues. Human herpesviruses range from mild childhood infections to known tumour viruses and 'trolls of transplantation'. Epstein-Barr virus was the first human herpesvirus to have its whole genome sequenced; GenBank now includes thousands of herpesvirus genomes. This review will cover some of the recent advances in our understanding of herpesvirus diversity and disease that have come about as a result of new sequencing technologies, such as target enrichment and long-read sequencing. It will also look at the problem of resolving mixed-genotype infections, whether with short or long-read sequencing methods; and conclude with some thoughts on the future of the field as herpesvirus population genomics becomes a reality.
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Affiliation(s)
- Charlotte J Houldcroft
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambs CB2 0QQ UK.
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA, UK.
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10
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Telford M, Navarro A, Santpere G. Whole genome diversity of inherited chromosomally integrated HHV-6 derived from healthy individuals of diverse geographic origin. Sci Rep 2018; 8:3472. [PMID: 29472617 PMCID: PMC5823862 DOI: 10.1038/s41598-018-21645-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
Human herpesviruses 6-A and -B (HHV-6A, HHV-6B) are ubiquitous in human populations worldwide. These viruses have been associated with several diseases such as multiple sclerosis, Hodgkin's lymphoma or encephalitis. Despite of the need to understand the genetic diversity and geographic stratification of these viruses, the availability of complete viral sequences from different populations is still limited. Here, we present nine new inherited chromosomally integrated HHV-6 sequences from diverse geographical origin which were generated through target DNA enrichment on lymphoblastoid cell lines derived from healthy individuals. Integration with available HHV-6 sequences allowed the assessment of HHV-6A and -6B phylogeny, patterns of recombination and signatures of natural selection. Analysis of the intra-species variability showed differences between A and B diversity levels and revealed that the HHV-6B reference (Z29) is an uncommon sequence, suggesting the need for an alternative reference sequence. Signs of geographical variation are present and more defined in HHV-6A, while they appear partly masked by recombination in HHV-6B. Finally, we conducted a scan for signatures of selection in protein coding genes that yielded at least 6 genes (4 and 2 respectively for the A and B species) showing significant evidence for accelerated evolution, and 1 gene showing evidence of positive selection in HHV-6A.
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Affiliation(s)
- Marco Telford
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.
- National Institute for Bioinformatics (INB), PRBB, Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Barcelona, Catalonia, Spain.
- Center for Genomic Regulation (CRG), PRBB, Barcelona, Catalonia, Spain.
| | - Gabriel Santpere
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
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11
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Tweedy JG, Escriva E, Topf M, Gompels UA. Analyses of Tissue Culture Adaptation of Human Herpesvirus-6A by Whole Genome Deep Sequencing Redefines the Reference Sequence and Identifies Virus Entry Complex Changes. Viruses 2017; 10:v10010016. [PMID: 29301233 PMCID: PMC5795429 DOI: 10.3390/v10010016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/23/2017] [Accepted: 12/26/2017] [Indexed: 11/18/2022] Open
Abstract
Tissue-culture adaptation of viruses can modulate infection. Laboratory passage and bacterial artificial chromosome (BAC)mid cloning of human cytomegalovirus, HCMV, resulted in genomic deletions and rearrangements altering genes encoding the virus entry complex, which affected cellular tropism, virulence, and vaccine development. Here, we analyse these effects on the reference genome for related betaherpesviruses, Roseolovirus, human herpesvirus 6A (HHV-6A) strain U1102. This virus is also naturally “cloned” by germline subtelomeric chromosomal-integration in approximately 1% of human populations, and accurate references are key to understanding pathological relationships between exogenous and endogenous virus. Using whole genome next-generation deep-sequencing Illumina-based methods, we compared the original isolate to tissue-culture passaged and the BACmid-cloned virus. This re-defined the reference genome showing 32 corrections and 5 polymorphisms. Furthermore, minor variant analyses of passaged and BACmid virus identified emerging populations of a further 32 single nucleotide polymorphisms (SNPs) in 10 loci, half non-synonymous indicating cell-culture selection. Analyses of the BAC-virus genome showed deletion of the BAC cassette via loxP recombination removing green fluorescent protein (GFP)-based selection. As shown for HCMV culture effects, select HHV-6A SNPs mapped to genes encoding mediators of virus cellular entry, including virus envelope glycoprotein genes gB and the gH/gL complex. Comparative models suggest stabilisation of the post-fusion conformation. These SNPs are essential to consider in vaccine-design, antimicrobial-resistance, and pathogenesis.
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Affiliation(s)
- Joshua G Tweedy
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
| | - Eric Escriva
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
- Institute for Structural and Molecular Biology, Department Biology, Birkbeck College University of London, London WC1E 7HX, UK.
| | - Maya Topf
- Institute for Structural and Molecular Biology, Department Biology, Birkbeck College University of London, London WC1E 7HX, UK.
| | - Ursula A Gompels
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
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12
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Tweedy JG, Prusty BK, Gompels UA. Use of whole genome deep sequencing to define emerging minority variants in virus envelope genes in herpesvirus treated with novel antimicrobial K21. Antiviral Res 2017; 146:201-204. [PMID: 28939478 DOI: 10.1016/j.antiviral.2017.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 02/07/2023]
Abstract
New antivirals are required to prevent rising antimicrobial resistance from replication inhibitors. The aim of this study was to analyse the range of emerging mutations in herpesvirus by whole genome deep sequencing. We tested human herpesvirus 6 treatment with novel antiviral K21, where evidence indicated distinct effects on virus envelope proteins. We treated BACmid cloned virus in order to analyse mechanisms and candidate targets for resistance. Illumina based next generation sequencing technology enabled analyses of mutations in 85 genes to depths of 10,000 per base detecting low prevalent minority variants (<1%). After four passages in tissue culture the untreated virus accumulated mutations in infected cells giving an emerging mixed population (45-73%) of non-synonymous SNPs in six genes including two envelope glycoproteins. Strikingly, treatment with K21 did not accumulate the passage mutations; instead a high frequency mutation was selected in envelope protein gQ2, part of the gH/gL complex essential for herpesvirus infection. This introduced a stop codon encoding a truncation mutation previously observed in increased virion production. There was reduced detection of the glycoprotein complex in infected cells. This supports a novel pathway for K21 targeting virion envelopes distinct from replication inhibition.
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Affiliation(s)
- Joshua G Tweedy
- Department of Pathogen Molecular Biology, London School Hygiene & Tropical Medicine, University of London, UK
| | - Bhupesh K Prusty
- Biocenter, Chair of Microbiology, University of Wurzberg, Germany
| | - Ursula A Gompels
- Department of Pathogen Molecular Biology, London School Hygiene & Tropical Medicine, University of London, UK.
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13
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Pontejo SM, Murphy PM. Chemokines encoded by herpesviruses. J Leukoc Biol 2017; 102:1199-1217. [PMID: 28848041 DOI: 10.1189/jlb.4ru0417-145rr] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/15/2022] Open
Abstract
Viruses use diverse strategies to elude the immune system, including copying and repurposing host cytokine and cytokine receptor genes. For herpesviruses, the chemokine system of chemotactic cytokines and receptors is a common source of copied genes. Here, we review the current state of knowledge about herpesvirus-encoded chemokines and discuss their possible roles in viral pathogenesis, as well as their clinical potential as novel anti-inflammatory agents or targets for new antiviral strategies.
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Affiliation(s)
- Sergio M Pontejo
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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14
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Kawamura Y, Ohye T, Miura H, Ihira M, Kato Y, Kurahashi H, Yoshikawa T. Analysis of the origin of inherited chromosomally integrated human herpesvirus 6 in the Japanese population. J Gen Virol 2017; 98:1823-1830. [PMID: 28699856 DOI: 10.1099/jgv.0.000834] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Integration of the complete human herpesvirus 6 (HHV-6) genome into the telomere of a chromosome has been reported in some individuals (inherited chromosomally integrated HHV-6; iciHHV-6). Since the proportion of iciHHV-6-positive individuals with integration in chromosome 22 is high in Japan, we hypothesized a founder effect. In this study, we sought to elucidate the reason for the high proportion of viral integrations into chromosome 22. We analyzed six cases of iciHHV-6A and two cases of iciHHV-6B, including one iciHHV-6A case with a matched sample from a father and one iciHHV-6B case with a matched sample from a mother. In iciHHV-6A, the same copy numbers of viral telomeric repeat sequences (TRS) and the same five microsatellite markers were detected in both the index case and paternal sample. Moreover, the same five microsatellite markers were demonstrated in four cases and the same copy numbers of viral TRS were demonstrated in two pairs of two cases. The present microsatellite analysis suggested that the viral genomes detected in some iciHHV-6A patients were derived from a common ancestral integration.
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Affiliation(s)
- Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan.,Present address: Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 1090340 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tamae Ohye
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan.,Department of Molecular Laboratory Medicine, Faculty of Medical Technology, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Masaru Ihira
- Faculty of Clinical Engineering, Fujita Health University School of Health Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Yuri Kato
- Department of Clinical Laboratory, Fujita Health University Hospital, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
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15
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Human Herpesvirus 6B Induces Hypomethylation on Chromosome 17p13.3, Correlating with Increased Gene Expression and Virus Integration. J Virol 2017; 91:JVI.02105-16. [PMID: 28298607 DOI: 10.1128/jvi.02105-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/03/2017] [Indexed: 12/21/2022] Open
Abstract
Human herpesvirus 6B (HHV-6B) is a neurotropic betaherpesvirus that achieves latency by integrating its genome into host cell chromosomes. Several viruses can induce epigenetic modifications in their host cells, but no study has investigated the epigenetic modifications induced by HHV-6B. This study analyzed methylation with an Illumina 450K array, comparing HHV-6B-infected and uninfected Molt-3 T cells 3 days postinfection. Bisulfite pyrosequencing was used to validate the Illumina results and to investigate methylation over time in vitro Expression of genes was investigated using quantitative PCR (qPCR), and virus integration was investigated with PCR. A total of 406 CpG sites showed a significant HHV-6B-induced change in methylation in vitro Remarkably, 86% (351/406) of these CpGs were located <1 Mb from chromosomal ends and were all hypomethylated in virus-infected cells. This was most evident at chromosome 17p13.3, where HHV-6B had induced CpG hypomethylation after 2 days of infection, possibly through TET2, which was found to be upregulated by the virus. In addition, virus-induced cytosine hydroxymethylation was observed. Genes located in the hypomethylated region at 17p13.3 showed significantly upregulated expression in HHV-6B-infected cells. A temporal experiment revealed HHV-6B integration in Molt-3 cell DNA 3 days after infection. The telomere at 17p has repeatedly been described as an integration site for HHV-6B, and we show for the first time that HHV-6B induces hypomethylation in this region during acute infection, which may play a role in the integration process, possibly by making the DNA more accessible.IMPORTANCE The ability to establish latency in the host is a hallmark of herpesviruses, but the mechanisms differ. Human herpesvirus 6B (HHV-6B) is known to establish latency through integration of its genome into the telomeric regions of host cells, with the ability to reactivate. Our study is the first to show that HHV-6B specifically induces hypomethylated regions close to the telomeres and that integrating viruses may use the host methylation machinery to facilitate their integration process. The results from this study contribute to knowledge of HHV-6B biology and virus-host interaction. This in turn will lead to further progress in our understanding of the underlying mechanisms by which HHV-6B contributes to pathological processes and may have important implications in both disease prevention and treatment.
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16
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Chromosomal integration of HHV-6A during non-productive viral infection. Sci Rep 2017; 7:512. [PMID: 28360414 PMCID: PMC5428774 DOI: 10.1038/s41598-017-00658-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/07/2017] [Indexed: 11/28/2022] Open
Abstract
Human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) are two different species of betaherpesviruses that integrate into sub-telomeric ends of human chromosomes, for which different prevalence rates of integration have been reported. It has been demonstrated that integrated viral genome is stable and is fully retained. However, study of chromosomally integrated viral genome in individuals carrying inherited HHV-6 (iciHHV-6) showed unexpected number of viral DR copies. Hence, we created an in vitro infection model and studied retention of full or partial viral genome over a period of time. We observed an exceptional event where cells retained viral direct repeats (DRs) alone in the absence of the full viral genome. Finally, we found evidence for non-telomeric integration of HHV-6A DR in both cultured cells and in an iciHHV-6 individual. Our results shed light on several novel features of HHV-6A chromosomal integration and provide valuable information for future screening techniques.
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17
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Wallaschek N, Sanyal A, Pirzer F, Gravel A, Mori Y, Flamand L, Kaufer BB. The Telomeric Repeats of Human Herpesvirus 6A (HHV-6A) Are Required for Efficient Virus Integration. PLoS Pathog 2016; 12:e1005666. [PMID: 27244446 PMCID: PMC4887096 DOI: 10.1371/journal.ppat.1005666] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/09/2016] [Indexed: 11/20/2022] Open
Abstract
Human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) are ubiquitous betaherpesviruses that infects humans within the first years of life and establishes latency in various cell types. Both viruses can integrate their genomes into telomeres of host chromosomes in latently infected cells. The molecular mechanism of viral integration remains elusive. Intriguingly, HHV-6A, HHV-6B and several other herpesviruses harbor arrays of telomeric repeats (TMR) identical to human telomere sequences at the ends of their genomes. The HHV-6A and HHV-6B genomes harbor two TMR arrays, the perfect TMR (pTMR) and the imperfect TMR (impTMR). To determine if the TMR are involved in virus integration, we deleted both pTMR and impTMR in the HHV-6A genome. Upon reconstitution, the TMR mutant virus replicated comparable to wild type (wt) virus, indicating that the TMR are not essential for HHV-6A replication. To assess the integration properties of the recombinant viruses, we established an in vitro integration system that allows assessment of integration efficiency and genome maintenance in latently infected cells. Integration of HHV-6A was severely impaired in the absence of the TMR and the virus genome was lost rapidly, suggesting that integration is crucial for the maintenance of the virus genome. Individual deletion of the pTMR and impTMR revealed that the pTMR play the major role in HHV-6A integration, whereas the impTMR only make a minor contribution, allowing us to establish a model for HHV-6A integration. Taken together, our data shows that the HHV-6A TMR are dispensable for virus replication, but are crucial for integration and maintenance of the virus genome in latently infected cells. Herpesviruses are ubiquitous pathogens that persist in the host for life. Two human herpesviruses (HHV-6A and HHV-6B) can integrate their genetic material into the telomeres of host chromosomes. Integration also occurs in germ cells, resulting in individuals that harbor the virus in every single cells of their body and transmit it to their offspring, a condition that affects about 1% of the human population. We set to elucidate the integration mechanism that allows these viruses to maintain their genome in infected cells. Intriguingly, HHV-6A, HHV-6B and several other herpesviruses harbor telomere sequences at the end of their genome. Removal of these sequences in the genome of HHV-6A revealed that the viral telomeres are crucial for the integration of this human herpesvirus. In addition, we demonstrate that the telomere sequences at the right and left end of the virus genome play different roles in the integration process. Taken together, our data sheds light on the integration mechanism that allows HHV-6A to integrate into somatic cells and to enter into the germ line.
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Affiliation(s)
- Nina Wallaschek
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Anirban Sanyal
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Fabian Pirzer
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Annie Gravel
- Division of Infectious Disease and Immunity, CHU de Québec Research Center, Quebec City, Quebec, Canada
| | - Yasuko Mori
- Division of Clinical Virology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Louis Flamand
- Division of Infectious Disease and Immunity, CHU de Québec Research Center, Quebec City, Quebec, Canada
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, Québec, Canada
| | - Benedikt B. Kaufer
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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18
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Clark D. Clinical and laboratory features of human herpesvirus 6 chromosomal integration. Clin Microbiol Infect 2016; 22:333-339. [DOI: 10.1016/j.cmi.2015.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/24/2015] [Indexed: 12/16/2022]
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19
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Zhang E, Cotton VE, Hidalgo-Bravo A, Huang Y, Bell AJ, Jarrett RF, Wilkie GS, Davison AJ, Nacheva EP, Siebert R, Majid A, Kelpanides I, Jayne S, Dyer MJ, Royle NJ. HHV-8-unrelated primary effusion-like lymphoma associated with clonal loss of inherited chromosomally-integrated human herpesvirus-6A from the telomere of chromosome 19q. Sci Rep 2016; 6:22730. [PMID: 26947392 PMCID: PMC4779988 DOI: 10.1038/srep22730] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 02/18/2016] [Indexed: 12/26/2022] Open
Abstract
Primary effusion lymphomas (PEL) are associated with human herpesvirus-8 (HHV-8) and usually occur in immunocompromised individuals. However, there are numerous reports of HHV-8-unrelated PEL-like lymphomas with unknown aetiology. Here we characterize an HHV-8-unrelated PEL-like lymphoma in an elderly woman who was negative for human immunodeficiency viruses 1 and 2, and hepatitis B and C. The woman was, however, a carrier of an inherited-chromosomally-integrated human herpesvirus-6A (iciHHV-6A) genome in one 19q telomere. The iciHHV-6A genome was complete in blood DNA, encoding a full set of protein-coding genes. Interestingly, the entire iciHHV-6A genome was absent from the HHV-8-unrelated-PEL-like lymphoma cells despite retention of both copies of chromosome 19. The somatic loss of the 19q-iciHHV-6A genome occurred very early during lymphoma development and we propose it occurred via telomere-loop formation and excision to release a circular viral genome that was subsequently lost. Whether release of the HHV-6A genome from the telomere contributed to lymphomagenesis, or was coincidental, remains unclear but this event may have deregulated the expression of HHV-6A or 19q genes or else disrupted telomere function. To establish the frequency and importance of iciHHV-6 loss from telomeres, the HHV-6 copy number should be assessed in tumours that arise in iciHHV-6 carriers.
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Affiliation(s)
- Enjie Zhang
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Victoria E Cotton
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Yan Huang
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Adam J Bell
- MRC - University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Ruth F Jarrett
- MRC - University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Gavin S Wilkie
- MRC - University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Andrew J Davison
- MRC - University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Ellie P Nacheva
- Cytogenetics Laboratory, Royal Free London NHS Foundation Trust, London, NW3 2PF, UK
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel &University Hospital Schleswig-Holstein, Campus Kiel, Schwanenweg 24, D-24105 Kiel, Germany
| | - Aneela Majid
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, LE1 7RH, UK
| | - Inga Kelpanides
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, LE1 7RH, UK
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, LE1 7RH, UK
| | - Martin J Dyer
- Ernest and Helen Scott Haematological Research Institute, Department of Cancer Studies, University of Leicester, Leicester, LE1 7RH, UK
| | - Nicola J Royle
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
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20
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Hill JA, HallSedlak R, Magaret A, Huang ML, Zerr DM, Jerome KR, Boeckh M. Efficient identification of inherited chromosomally integrated human herpesvirus 6 using specimen pooling. J Clin Virol 2016; 77:71-6. [PMID: 26921738 DOI: 10.1016/j.jcv.2016.02.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/03/2016] [Accepted: 02/16/2016] [Indexed: 02/03/2023]
Abstract
BACKGROUND Human herpesvirus 6 (HHV-6) has a unique ability to integrate into chromosomal telomeres. Vertical transmission via germ cell integration results in offspring with inherited chromosomally integrated (ci)HHV-6 in all nucleated cells, affecting ∼1% of the population. OBJECTIVES Inherited ciHHV-6 may be a direct or indirect mediator of human disease, but efficient identification of affected individuals is a fundamental roadblock to larger studies exploring the clinical importance of this condition. STUDY DESIGN A group testing strategy was designed to efficiently identify individuals with inherited ciHHV-6. DNA was extracted from 2496 cellular samples from hematopoietic cell transplant (HCT) donor-recipient pairs. Pools of 12 samples were screened for HHV-6 DNA with quantitative (q)PCR. Individual samples from high positive pools were tested with qPCR, and high positive individual samples were tested for inherited ciHHV-6 using droplet digital (dd)PCR to determine HHV-6 DNA copies/cellular genome. RESULTS Thirty-one pools had high positive HHV-6 DNA detection with >10(3) HHV-6 DNA copies/μg. Each pool had one sample with >10(4) copies/μg HHV-6 DNA. Inherited ciHHV-6 was confirmed by ddPCR in every high positive sample (>10(3) HHV-6 DNA copies/μg), yielding a prevalence of 1.5% in HCT recipients and 0.96% in donors. We performed 580 qPCR tests to screen 2496 samples for inherited ciHHV-6, a 77% reduction in testing. CONCLUSIONS Inherited ciHHV-6 can be efficiently identified by specimen pooling coupled with modern molecular techniques. This algorithm can be used to facilitate cost-effective identification of patients with inherited ciHHV-6, thereby removing a major hurdle for large-scale study of its clinical impact.
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Affiliation(s)
- Joshua A Hill
- Department of Medicine, University of Washington, United States; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, United States.
| | - Ruth HallSedlak
- Department of Laboratory Medicine, University of Washington, United States
| | - Amalia Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, United States; Department of Laboratory Medicine, University of Washington, United States
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, United States
| | - Danielle M Zerr
- Department of Medicine, University of Washington, United States; Seattle Children's Research Institute, Seattle, WA, United States
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, United States; Department of Laboratory Medicine, University of Washington, United States
| | - Michael Boeckh
- Department of Medicine, University of Washington, United States; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, United States
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21
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Tweedy J, Spyrou MA, Pearson M, Lassner D, Kuhl U, Gompels UA. Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection. Viruses 2016; 8:v8010019. [PMID: 26784220 PMCID: PMC4728579 DOI: 10.3390/v8010019] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/25/2015] [Accepted: 12/01/2015] [Indexed: 12/23/2022] Open
Abstract
Human herpesvirus-6A and B (HHV-6A, HHV-6B) have recently defined endogenous genomes, resulting from integration into the germline: chromosomally-integrated “CiHHV-6A/B”. These affect approximately 1.0% of human populations, giving potential for virus gene expression in every cell. We previously showed that CiHHV-6A was more divergent than CiHHV-6B by examining four genes in 44 European CiHHV-6A/B cardiac/haematology patients. There was evidence for gene expression/reactivation, implying functional non-defective genomes. To further define the relationship between HHV-6A and CiHHV-6A we used next-generation sequencing to characterize genomes from three CiHHV-6A cardiac patients. Comparisons to known exogenous HHV-6A showed CiHHV-6A genomes formed a separate clade; including all 85 non-interrupted genes and necessary cis-acting signals for reactivation as infectious virus. Greater single nucleotide polymorphism (SNP) density was defined in 16 genes and the direct repeats (DR) terminal regions. Using these SNPs, deep sequencing analyses demonstrated superinfection with exogenous HHV-6A in two of the CiHHV-6A patients with recurrent cardiac disease. Characterisation of the integration sites in twelve patients identified the human chromosome 17p subtelomere as a prevalent site, which had specific repeat structures and phylogenetically related CiHHV-6A coding sequences indicating common ancestral origins. Overall CiHHV-6A genomes were similar, but distinct from known exogenous HHV-6A virus, and have the capacity to reactivate as emerging virus infections.
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Affiliation(s)
- Joshua Tweedy
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
| | - Maria Alexandra Spyrou
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
| | - Max Pearson
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
| | - Dirk Lassner
- Institute of Cardiac diagnostics (IKDT), Charite University, D-12203 Berlin, Germany.
| | - Uwe Kuhl
- Institute of Cardiac diagnostics (IKDT), Charite University, D-12203 Berlin, Germany.
| | - Ursula A Gompels
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
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22
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Agut H, Bonnafous P, Gautheret-Dejean A. Laboratory and clinical aspects of human herpesvirus 6 infections. Clin Microbiol Rev 2015; 28:313-35. [PMID: 25762531 PMCID: PMC4402955 DOI: 10.1128/cmr.00122-14] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Human herpesvirus 6 (HHV-6) is a widespread betaherpesvirus which is genetically related to human cytomegalovirus (HCMV) and now encompasses two different species: HHV-6A and HHV-6B. HHV-6 exhibits a wide cell tropism in vivo and, like other herpesviruses, induces a lifelong latent infection in humans. As a noticeable difference with respect to other human herpesviruses, genomic HHV-6 DNA is covalently integrated into the subtelomeric region of cell chromosomes (ciHHV-6) in about 1% of the general population. Although it is infrequent, this may be a confounding factor for the diagnosis of active viral infection. The diagnosis of HHV-6 infection is performed by both serologic and direct methods. The most prominent technique is the quantification of viral DNA in blood, other body fluids, and organs by means of real-time PCR. Many active HHV-6 infections, corresponding to primary infections, reactivations, or exogenous reinfections, are asymptomatic. However, the virus may be the cause of serious diseases, particularly in immunocompromised individuals. As emblematic examples of HHV-6 pathogenicity, exanthema subitum, a benign disease of infancy, is associated with primary infection, whereas further virus reactivations can induce severe encephalitis cases, particularly in hematopoietic stem cell transplant recipients. Generally speaking, the formal demonstration of the causative role of HHV-6 in many acute and chronic human diseases is difficult due to the ubiquitous nature of the virus, chronicity of infection, existence of two distinct species, and limitations of current investigational tools. The antiviral compounds ganciclovir, foscarnet, and cidofovir are effective against active HHV-6 infections, but the indications for treatment, as well as the conditions of drug administration, are not formally approved to date. There are still numerous pending questions about HHV-6 which should stimulate future research works on the pathophysiology, diagnosis, and therapy of this remarkable human virus.
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Affiliation(s)
- Henri Agut
- Sorbonne Universités, UPMC, CIMI-Paris UMRS CR7, PVI Team, Paris, France INSERM, CIMI-Paris U1135, PVI Team, Paris, France AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Service de Virologie, Paris, France
| | - Pascale Bonnafous
- Sorbonne Universités, UPMC, CIMI-Paris UMRS CR7, PVI Team, Paris, France INSERM, CIMI-Paris U1135, PVI Team, Paris, France
| | - Agnès Gautheret-Dejean
- Sorbonne Universités, UPMC, CIMI-Paris UMRS CR7, PVI Team, Paris, France INSERM, CIMI-Paris U1135, PVI Team, Paris, France AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Service de Virologie, Paris, France Université René Descartes, Faculté de Pharmacie, Laboratoire de Microbiologie UPRES EA 4065, Paris, France
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23
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Complete Genome Sequence of the Human Herpesvirus 6A Strain AJ from Africa Resembles Strain GS from North America. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01498-14. [PMID: 25676750 PMCID: PMC4333650 DOI: 10.1128/genomea.01498-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The genome sequence of human herpesvirus 6A (HHV-6A) strain AJ was determined in a comparison of target enrichment and long-range PCR using next-generation sequencing methodologies. The analyses show 85 predicted open reading frames (ORFs), conservation with sequenced HHV-6A reference strain U1102, and closest identity to the recently determined GS strain, despite different geographic origins (United States and Gambia).
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