1
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Barrie W, Yang Y, Irving-Pease EK, Attfield KE, Scorrano G, Jensen LT, Armen AP, Dimopoulos EA, Stern A, Refoyo-Martinez A, Pearson A, Ramsøe A, Gaunitz C, Demeter F, Jørkov MLS, Møller SB, Springborg B, Klassen L, Hyldgård IM, Wickmann N, Vinner L, Korneliussen TS, Allentoft ME, Sikora M, Kristiansen K, Rodriguez S, Nielsen R, Iversen AKN, Lawson DJ, Fugger L, Willerslev E. Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations. Nature 2024; 625:321-328. [PMID: 38200296 PMCID: PMC10781639 DOI: 10.1038/s41586-023-06618-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/06/2023] [Indexed: 01/12/2024]
Abstract
Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.
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Affiliation(s)
- William Barrie
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yaoling Yang
- Department of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
| | - Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kathrine E Attfield
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lise Torp Jensen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Angelos P Armen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | | | - Aaron Stern
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Alba Refoyo-Martinez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Abigail Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Charleen Gaunitz
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Musée de l'Homme, Paris, France
| | - Marie Louise S Jørkov
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Lutz Klassen
- Museum Østdanmark-Djursland og Randers, Randers, Denmark
| | | | | | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Santiago Rodriguez
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Astrid K N Iversen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK.
| | - Daniel J Lawson
- Department of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK.
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK.
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK.
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark.
- MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK.
| | - Eske Willerslev
- Department of Zoology, University of Cambridge, Cambridge, UK.
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
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2
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de-Dios T, Scheib CL, Houldcroft CJ. An Adagio for Viruses, Played Out on Ancient DNA. Genome Biol Evol 2023; 15:evad047. [PMID: 36930529 PMCID: PMC10063219 DOI: 10.1093/gbe/evad047] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/16/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Studies of ancient DNA have transformed our understanding of human evolution. Paleogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic, and pandemic pathogens. Viruses-and in particular those with single- or double-stranded DNA genomes-are an important part of the paleogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly evolving viruses which cause disease. In this review, we revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We look at how paleogenomics works for viral pathogens, such as the need for careful precautions against modern contamination and robust computational pipelines to identify and analyze authenticated viral sequences. We discuss the insights into virus evolution which have been gained through paleogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.
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Affiliation(s)
- Toni de-Dios
- Institute of Genomics, University of Tartu, Estonia
| | - Christiana L Scheib
- Institute of Genomics, University of Tartu, Estonia
- St. John's College, University of Cambridge, United Kingdom
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3
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Forni D, Cagliani R, Clerici M, Sironi M. Disease-causing human viruses: novelty and legacy. Trends Microbiol 2022; 30:1232-1242. [PMID: 35902319 DOI: 10.1016/j.tim.2022.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023]
Abstract
About 270 viruses are known to infect humans. Some of these viruses have been known for centuries, whereas others have recently emerged. During their evolutionary history, humans have moved out of Africa to populate the world. In historical times, human migrations resulted in the displacement of large numbers of people. All these events determined the movement and dispersal of human-infecting viruses. Technological advances have resulted in the characterization of the genetic variability of human viruses, both in extant and in archaeological samples. Field studies investigated the diversity of viruses hosted by other animals. In turn, these advances provided insight into the evolutionary history of human viruses back in time and defined the key events through which they originated and spread.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy; Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
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4
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Guellil M, van Dorp L, Inskip SA, Dittmar JM, Saag L, Tambets K, Hui R, Rose A, D’Atanasio E, Kriiska A, Varul L, Koekkelkoren AMHC, Goldina RD, Cessford C, Solnik A, Metspalu M, Krause J, Herbig A, Robb JE, Houldcroft CJ, Scheib CL. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. SCIENCE ADVANCES 2022; 8:eabo4435. [PMID: 35895820 PMCID: PMC9328674 DOI: 10.1126/sciadv.abo4435] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/10/2022] [Indexed: 05/05/2023]
Abstract
Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.
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Affiliation(s)
- Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology and Ancient History, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Jenna M. Dittmar
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Aberdeen, UK
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Alan Turing Institute, 2QR, John Dodson House, 96 Euston Rd., London NW1 2DB, UK
| | - Alice Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | | | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia
| | - Liivi Varul
- Archaeological Research Collection, School of Humanities, Tallinn University, Tallinn 10130, Estonia
| | | | - Rimma D. Goldina
- Department History of Udmurtia, Archaeology and Ethnology, Udmurt State University, 1, Universitetskaya St. 1, 426034 Izhevsk, Russia
| | - Craig Cessford
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010 Estonia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Christiana L. Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
- St. John’s College, University of Cambridge, Cambridge, CB2 1TP, UK
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5
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Tommasi C, Breuer J. The Biology of Varicella-Zoster Virus Replication in the Skin. Viruses 2022; 14:982. [PMID: 35632723 PMCID: PMC9147561 DOI: 10.3390/v14050982] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 02/07/2023] Open
Abstract
The replication of varicella-zoster virus (VZV) in skin is critical to its pathogenesis and spread. Primary infection causes chickenpox, which is characterised by centrally distributed skin blistering lesions that are rich in infectious virus. Cell-free virus in the cutaneous blistering lesions not only spreads to cause further cases, but infects sensory nerve endings, leading to the establishment of lifelong latency in sensory and autonomic ganglia. The reactivation of virus to cause herpes zoster is again characterised by localised painful skin blistering rash containing infectious virus. The development of in vitro and in vivo models of VZV skin replication has revealed aspects of VZV replication and pathogenesis in this important target organ and improved our understanding of the vaccine strain vOKa attenuation. In this review, we outline the current knowledge on VZV interaction with host signalling pathways, the viral association with proteins associated with epidermal terminal differentiation, and how these interconnect with the VZV life cycle to facilitate viral replication and shedding.
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Affiliation(s)
- Cristina Tommasi
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Judith Breuer
- Department of Infection, Institute of Child Health, University College London, London WC1N 1EH, UK
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6
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Hwang HR, Kang SH, Lee CH. Genetic changes in plaque-purified varicella vaccine strain Suduvax during in vitro propagation in cell culture. J Microbiol 2021; 59:702-707. [PMID: 34061341 DOI: 10.1007/s12275-021-1062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Infection by varicella-zoster virus (VZV) can be prevented by using live attenuated vaccines. VZV vaccine strains are known to evolve rapidly in vivo, however, their genetic and biological effects are not known. In this study, the plaque-purified vaccine strain Suduvax (PPS) was used to understand the genetic changes that occur during the process of propagation in in vitro cell culture. Full genome sequences of three different passages (p4, p30, and p60) of PPS were determined and compared for genetic changes. Mutations were found at 59 positions. The number of genetically polymorphic sites (GPS) and the average of minor allele frequency (MAF) at GPSs were not significantly altered after passaging in cell culture up to p60. The number of variant nucleotide positions (VNPs), wherein GPS was found in at least one passage of PPS, was 149. Overall, MAF changed by less than 5% at 52 VNPs, increased by more than 5% at 42 VNPs, and decreased by more than 5% at 55 VNPs in p60, compared with that seen in p4. More complicated patterns of changes in MAF were observed when genetic polymorphism at 149 VNPs was analyzed among the three passages. However, MAF decreased and mixed genotypes became unequivocally fixed to vaccine type in 23 vaccine-specific positions in higher passages of PPS. Plaque-purified Suduvax appeared to adapt to better replication during in vitro cell culture. Further studies with other vaccine strains and in vivo studies will help to understand the evolution of the VZV vaccine.
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Affiliation(s)
- Hye Rim Hwang
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Se Hwan Kang
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Chan Hee Lee
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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7
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Forni D, Pontremoli C, Clerici M, Pozzoli U, Cagliani R, Sironi M. Recent Out-of-Africa Migration of Human Herpes Simplex Viruses. Mol Biol Evol 2021; 37:1259-1271. [PMID: 31917410 DOI: 10.1093/molbev/msaa001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results indicated that HSV-1 populations have limited geographic structure and the most evident clustering by geography is likely due to recent bottlenecks. For HSV-2, the only level of population structure is accounted for by the so-called "worldwide" and "African" lineages. Analysis of ancestry components and nucleotide diversity, however, did not support the view that the worldwide lineage followed early humans during out-of-Africa dispersal. Although phylogeographic analysis confirmed an African origin for both viruses, molecular dating with a method that corrects for the time-dependent rate phenomenon indicated that HSV-1 and HSV-2 migrated from Africa in relatively recent times. In particular, we estimated that the HSV-2 worldwide lineage left the continent in the 18th century, which corresponds to the height of the transatlantic slave trade, possibly explaining the high prevalence of HSV-2 in the Americas (second highest after Africa). The limited geographic clustering of HSV-1 makes it difficult to date its exit from Africa. The split between the basal clade, containing mostly African sequences, and all other strains was dated at ∼5,000 years ago. Our data do not imply that herpes simplex viruses did not infect early humans but show that the worldwide distribution of circulating strains is the result of relatively recent events.
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Affiliation(s)
- Diego Forni
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Lecco, Italy
| | | | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Uberto Pozzoli
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Lecco, Italy
| | - Rachele Cagliani
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Lecco, Italy
| | - Manuela Sironi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Lecco, Italy
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8
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Pontremoli C, Forni D, Clerici M, Cagliani R, Sironi M. Possible European Origin of Circulating Varicella Zoster Virus Strains. J Infect Dis 2021; 221:1286-1294. [PMID: 31051029 DOI: 10.1093/infdis/jiz227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/02/2019] [Indexed: 11/13/2022] Open
Abstract
Varicella zoster virus (VZV) is the causative agent of chickenpox and shingles. The geographic distribution of VZV clades was taken as evidence that VZV migrated out of Africa with human populations. We show that extant VZV strains most likely originated in Europe and not in Africa. Europe was also identified as the ancestral location for most internal nodes of the VZV phylogeny, including the ancestor of clade 5 strains. We also show that strains from clades 1, 2, 3, and 5 derived a major proportion of their ancestry from each of 4 ancestral populations. Conversely, viruses from other clades displayed variable levels of admixture. Some low-level admixture was also observed for clade 5 genomes, but only for non-African viruses. This pattern indicates that the clade 5 VZV strains do not represent recent introductions from Africa due to migratory fluxes. These data have also relevance for the definition and classification of VZV clades.
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Affiliation(s)
- Chiara Pontremoli
- Istituto di ricovero e cura a carattere scientifico (IRCCS) E. Medea, Bioinformatics, Bosisio Parini, Milan, Italy
| | - Diego Forni
- Istituto di ricovero e cura a carattere scientifico (IRCCS) E. Medea, Bioinformatics, Bosisio Parini, Milan, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Rachele Cagliani
- Istituto di ricovero e cura a carattere scientifico (IRCCS) E. Medea, Bioinformatics, Bosisio Parini, Milan, Italy
| | - Manuela Sironi
- Istituto di ricovero e cura a carattere scientifico (IRCCS) E. Medea, Bioinformatics, Bosisio Parini, Milan, Italy
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9
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McElhaney JE, Verschoor C, Pawelec G. Zoster Vaccination in Older Adults: Efficacy and Public Health Implications. J Gerontol A Biol Sci Med Sci 2020; 74:1239-1243. [PMID: 30945744 DOI: 10.1093/gerona/glz085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Indexed: 12/18/2022] Open
Abstract
Shingles and its most common disabling complication, post-herpetic neuralgia, represent a serious public health challenge in the older population. The decline in the T-cell-mediated immune response to varicella zoster virus after age 50 is clearly associated with increased risk of viral reactivation, causing an acutely painful zoster rash, which may have a severe prodrome of dermatomal pain and persist as seriously debilitating post-herpetic neuralgia well beyond the resolution of the rash. However, new vaccines and adjuvants are being developed and trialed and are now more effective in preventing shingles and the sequelae of post-herpetic neuralgia. Those vaccines that possess the ability to enhance antigen presentation and reverse memory T-cell exhaustion, as well as diminish the immune suppressive effects of regulatory T cells, are most likely to be effective in older adults.
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Affiliation(s)
| | - Chris Verschoor
- Health Sciences North Research Institute, Sudbury, Ontario.,McMaster University, Hamilton, Ontario, Canada
| | - Graham Pawelec
- Health Sciences North Research Institute, Sudbury, Ontario.,Department of Immunology, University of Tübingen, Tübingen, Germany
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10
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Alizon S, Bravo IG, Farrell PJ, Roberts S. Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence. Philos Trans R Soc Lond B Biol Sci 2020; 374:20190041. [PMID: 30955496 DOI: 10.1098/rstb.2019.0041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
One out of 10 cancers is estimated to arise from infections by a handful of oncogenic viruses. These infectious cancers constitute an opportunity for primary prevention through immunization against the viral infection, for early screening through molecular detection of the infectious agent, and potentially for specific treatments, by targeting the virus as a marker of cancer cells. Accomplishing these objectives will require a detailed understanding of the natural history of infections, the mechanisms by which the viruses contribute to disease, the mutual adaptation of viruses and hosts, and the possible viral evolution in the absence and in the presence of the public health interventions conceived to target them. This issue showcases the current developments in experimental tissue-like and animal systems, mathematical models and evolutionary approaches to understand DNA oncoviruses. Our global aim is to provide proximate explanations to the present-day interface and interactions between virus and host, as well as ultimate explanations about the adaptive value of these interactions and about the evolutionary pathways that have led to the current malignant phenotype of oncoviral infections. This article is part of the theme issue 'Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses'.
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Affiliation(s)
- Samuel Alizon
- 1 French National Center for Scientific Research (CNRS), Laboratory MIVEGEC (CNRS, IRD, UM) , 34394 Montpellier , France
| | - Ignacio G Bravo
- 1 French National Center for Scientific Research (CNRS), Laboratory MIVEGEC (CNRS, IRD, UM) , 34394 Montpellier , France
| | | | - Sally Roberts
- 3 Institute of Cancer and Genomic Sciences, University of Birmingham , Birmingham B15 2SY , UK
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11
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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: 1.4] [Reference Citation Analysis] [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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12
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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: 1.0] [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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13
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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: 2.3] [Reference Citation Analysis] [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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14
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Breuer J. Molecular Genetic Insights Into Varicella Zoster Virus (VZV), the vOka Vaccine Strain, and the Pathogenesis of Latency and Reactivation. J Infect Dis 2019; 218:S75-S80. [PMID: 30247591 DOI: 10.1093/infdis/jiy279] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic tools for molecular typing of varicella zoster virus (VZV) have been used to understand the spread of virus, to differentiate wild-type and vaccine strains, and to understand the natural history of VZV infection in its cognate host. Molecular genetics has identified 7 clades of VZV (1-6 and 9), with 2 more mooted. Differences between the vOka vaccine strain and wild-type VZVs have been used to distinguish the cause of postimmunization events and to provide insight into the natural history of VZV infections. Importantly molecular genetics has shown that reinfection with establishment of latency by the reinfecting strain is common, that dual infections with different viruses can occur, and that reactivation of the superinfecting genotype can both occur. Whole-genome sequencing of the vOka vaccine has been used to show that vesicles form from a single virion, that latency is established within a few days of inoculation, and that all vaccine strains are capable of establishing latency and reactivating. Novel molecular tools have characterized the transcripts expressed during latent infection in vitro.
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Affiliation(s)
- Judith Breuer
- Division of Infection and Immunity, University College London, United Kingdom
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15
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Breuer J. The Origin and Migration of Varicella Zoster Virus Strains. J Infect Dis 2019; 221:1213-1215. [DOI: 10.1093/infdis/jiz232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Judith Breuer
- Division of Infection and Immunity, University College London, United Kingdom
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16
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Fulop T, Franceschi C, Hirokawa K, Pawelec G. Immunosenescence Modulation by Vaccination. HANDBOOK OF IMMUNOSENESCENCE 2019. [PMCID: PMC7121048 DOI: 10.1007/978-3-319-99375-1_71] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A decline in immune function is a hallmark of aging that leads to complicated illness from a variety of infectious diseases, cancer and other immune-mediated disorders, and may limit the ability to appropriately respond to vaccination. How vaccines might alter the senescent immune response and what are the immune correlates of protection will be addressed from the perspective of (1) stimulating a previously primed response as in the case of vaccines for seasonal influenza and herpes zoster, (2) priming the response to novel antigens such as pandemic influenza or West Nile virus, (3) vaccination against bacterial pathogens such as pneumococcus and pertussis, (4) vaccines against bacterial toxins such as tetanus and Clostridium difficile, and (5) vaccine approaches to mitigate effects of cytomegalovirus on immune senescence. New or improved vaccines developed over recent years demonstrate the considerable opportunity to improve current vaccines and develop new vaccines as a preventive approach to a variety of diseases in older adults. Strategies for selecting appropriate immunologic targets for new vaccine development and evaluating how vaccines may alter the senescent immune response in terms of potential benefits and risks in the preclinical and clinical trial phases of vaccine development will be discussed.
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Affiliation(s)
- Tamas Fulop
- Division of Geriatrics Research Center on Aging, University of Sherbrooke Department of Medicine, Sherbrooke, QC Canada
| | - Claudio Franceschi
- Department of Experimental Pathology, University of Bologna, Bologna, Italy
| | | | - Graham Pawelec
- Center for Medical Research, University of Tübingen, Tübingen, Germany
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17
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Doroshenko A, Pepperell CS, Heffernan C, Egedahl ML, Mortimer TD, Smith TM, Bussan HE, Tyrrell GJ, Long R. Epidemiological and genomic determinants of tuberculosis outbreaks in First Nations communities in Canada. BMC Med 2018; 16:128. [PMID: 30086755 PMCID: PMC6081810 DOI: 10.1186/s12916-018-1112-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 06/27/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In Canada, tuberculosis disproportionately affects foreign-born and First Nations populations. Within First Nations' peoples, a high proportion of cases occur in association with outbreaks. Tuberculosis transmission in the context of outbreaks is thought to result from the convergence of several factors including characteristics of the cases, contacts, the environment, and the pathogen. METHODS We examined the epidemiological and genomic determinants of two well-characterized tuberculosis outbreaks attributed to two super-spreaders among First Nations in the province of Alberta. These outbreaks were associated with two distinct DNA fingerprints (restriction fragment-length polymorphisms or RFLPs 0.0142 and 0.0728). We compared outbreak isolates with endemic isolates not spatio-temporarily linked to outbreak cases. We extracted epidemiological variables pertaining to tuberculosis cases and contacts from individual public health records and the provincial tuberculosis registry. We conducted group analyses using parametric and non-parametric statistical tests. We carried out whole-genome sequencing and bioinformatic analysis using validated protocols. RESULTS We observed differences between outbreak and endemic groups in the mean number of total and child-aged contacts and the number of contacts with new positive and converted tuberculin skin tests in all group comparisons (p < 0.05). Differences were also detected in the proportion of cases with cavitation on a chest radiograph and the mean number of close contacts in selected group comparisons (p < 0.02). A phylogenetic network analysis of whole-genome sequencing data indicated that most outbreak and endemic strains were closely related to the source case for the 0.0142 fingerprint. For the 0.0728 fingerprint, the source case haplotype was circulating among endemic cases prior to the outbreak. Genetic and temporal distances were not correlated for either RFLP 0.0142 (r2 = - 0.05) or RFLP 0.0728 (r2 = 0.09) when all isolates were analyzed. CONCLUSIONS We found no evidence that endemic strains acquired mutations resulting in their emergence in outbreak form. We conclude that the propagation of these outbreaks was likely driven by the combination of characteristics of the source cases, contacts, and the environment. The role of whole-genome sequencing in understanding mycobacterial evolution and in assisting public health authorities in conducting contact investigations and managing outbreaks is important and expected to grow in the future.
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Affiliation(s)
- Alexander Doroshenko
- Division of Preventive Medicine, Department of Medicine, Faculty of Medicine and Dentistry and School of Public Health, University of Alberta, Edmonton, Canada.
| | - Caitlin S Pepperell
- Departments of Medicine (Infectious Diseases) and Medical Microbiology & Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA
| | - Courtney Heffernan
- Department of Medicine, Faculty of Medicine and Dentistry and TB Program Evaluation and Research Unit, University of Alberta, Edmonton, Canada
| | - Mary Lou Egedahl
- Department of Medicine, Faculty of Medicine and Dentistry and TB Program Evaluation and Research Unit, University of Alberta, Edmonton, Canada
| | - Tatum D Mortimer
- Departments of Medicine (Infectious Diseases) and Medical Microbiology & Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA
| | - Tracy M Smith
- Departments of Medicine (Infectious Diseases) and Medical Microbiology & Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA
| | - Hailey E Bussan
- Departments of Medicine (Infectious Diseases) and Medical Microbiology & Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA
| | - Gregory J Tyrrell
- Department of Laboratory Medicine and Pathology, University of Alberta, Provincial Laboratory for Public Health, Alberta Health Services, Edmonton, Canada
| | - Richard Long
- Department of Medicine, Faculty of Medicine and Dentistry and TB Program Evaluation and Research Unit, University of Alberta, Edmonton, Canada
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18
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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: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [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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19
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Bryant NA, Wilkie GS, Russell CA, Compston L, Grafham D, Clissold L, McLay K, Medcalf L, Newton R, Davison AJ, Elton DM. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks. Transbound Emerg Dis 2018; 65:817-832. [PMID: 29423949 PMCID: PMC5947664 DOI: 10.1111/tbed.12809] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Indexed: 12/14/2022]
Abstract
Equine herpesvirus 1 (EHV‐1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV‐1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term “neuropathic strain,” even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understanding of EHV‐1 diversity in the field, 78 EHV‐1 strains isolated over a period of 35 years were sequenced. The great majority of isolates originated from the United Kingdom and included in the collection were low passage isolates from respiratory, abortigenic and neurological outbreaks. Phylogenetic analysis of regions spanning 80% of the genome showed that up to 13 viral clades have been circulating in the United Kingdom and that most of these are continuing to circulate. Abortion isolates grouped into nine clades, and neurological isolates grouped into five. Most neurological isolates had the N752D substitution, whereas most abortion isolates did not, although three of the neurological isolates from linked outbreaks had a different polymorphism. Finally, bioinformatic analysis suggested that recombination has occurred between EHV‐1 clades, between EHV‐1 and equine herpesvirus 4, and between EHV‐1 and equine herpesvirus 8.
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Affiliation(s)
- N A Bryant
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - G S Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - C A Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - L Compston
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - D Grafham
- Sheffield Children's NHS Foundation Trust, Sheffield, South Yorkshire, UK
| | - L Clissold
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - K McLay
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - L Medcalf
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - R Newton
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - A J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - D M Elton
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
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20
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Warren-Gash C, Forbes H, Breuer J. Varicella and herpes zoster vaccine development: lessons learned. Expert Rev Vaccines 2017; 16:1191-1201. [PMID: 29047317 PMCID: PMC5942150 DOI: 10.1080/14760584.2017.1394843] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/17/2017] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Before vaccination, varicella zoster virus (VZV), which is endemic worldwide, led to almost universal infection. This neurotropic virus persists lifelong by establishing latency in sensory ganglia, where its reactivation is controlled by VZV-specific T-cell immunity. Lifetime risk of VZV reactivation (zoster) is around 30%. Vaccine development was galvanised by the economic and societal burden of VZV, including debilitating zoster complications that largely affect older individuals. Areas covered: We describe the story of development, licensing and implementation of live attenuated vaccines against varicella and zoster. We consider the complex backdrop of VZV virology, pathogenesis and immune responses in the absence of suitable animal models and examine the changing epidemiology of VZV disease. We review the vaccines' efficacy, safety, effectiveness and coverage using evidence from trials, observational studies from large routine health datasets and clinical post-marketing surveillance studies and outline newer developments in subunit and inactivated vaccines. Expert commentary: Safe and effective, varicella and zoster vaccines have already made major inroads into reducing the burden of VZV disease globally. As these live vaccines have the potential to reactivate and cause clinical disease, developing alternatives that do not establish latency is an attractive prospect but will require better understanding of latency mechanisms.
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Affiliation(s)
- Charlotte Warren-Gash
- Faculty of Epidemiology & Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Harriet Forbes
- Faculty of Epidemiology & Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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21
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Alizon S, Murall CL, Bravo IG. Why Human Papillomavirus Acute Infections Matter. Viruses 2017; 9:v9100293. [PMID: 28994707 PMCID: PMC5691644 DOI: 10.3390/v9100293] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 09/25/2017] [Accepted: 10/02/2017] [Indexed: 02/06/2023] Open
Abstract
Most infections by human papillomaviruses (HPVs) are `acute', that is non-persistent. Yet, for HPVs, as for many other oncoviruses, there is a striking gap between our detailed understanding of chronic infections and our limited data on the early stages of infection. Here we argue that studying HPV acute infections is necessary and timely. Focusing on early interactions will help explain why certain infections are cleared while others become chronic or latent. From a molecular perspective, descriptions of immune effectors and pro-inflammatory pathways during the initial stages of infections have the potential to lead to novel treatments or to improved handling algorithms. From a dynamical perspective, adopting concepts from spatial ecology, such as meta-populations or meta-communities, can help explain why HPV acute infections sometimes last for years. Furthermore, cervical cancer screening and vaccines impose novel iatrogenic pressures on HPVs, implying that anticipating any viral evolutionary response remains essential. Finally, hints at the associations between HPV acute infections and fertility deserve further investigation given their high, worldwide prevalence. Overall, understanding asymptomatic and benign infections may be instrumental in reducing HPV virulence.
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Affiliation(s)
- Samuel Alizon
- MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), 911 avenue Agropolis, 34394 Montpellier CEDEX 5, France.
| | - Carmen Lía Murall
- MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), 911 avenue Agropolis, 34394 Montpellier CEDEX 5, France.
| | - Ignacio G Bravo
- MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), 911 avenue Agropolis, 34394 Montpellier CEDEX 5, France.
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22
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Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion. J Virol 2017; 91:JVI.01141-17. [PMID: 28747504 DOI: 10.1128/jvi.01141-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/21/2017] [Indexed: 12/19/2022] Open
Abstract
The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture.IMPORTANCE Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple in vitro passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture.
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23
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Impact of Type I Interferon on the Safety and Immunogenicity of an Experimental Live-Attenuated Herpes Simplex Virus 1 Vaccine in Mice. J Virol 2017; 91:JVI.02342-16. [PMID: 28122977 DOI: 10.1128/jvi.02342-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022] Open
Abstract
Viral fitness dictates virulence and capacity to evade host immune defenses. Understanding the biological underpinnings of such features is essential for rational vaccine development. We have previously shown that the live-attenuated herpes simplex virus 1 (HSV-1) mutant lacking the nuclear localization signal (NLS) on the ICP0 gene (0ΔNLS) is sensitive to inhibition by interferon beta (IFN-β) in vitro and functions as a highly efficacious experimental vaccine. Here, we characterize the host immune response and in vivo pathogenesis of HSV-1 0ΔNLS relative to its fully virulent parental strain in C57BL/6 mice. Additionally, we explore the role of type 1 interferon (IFN-α/β) signaling on virulence and immunogenicity of HSV-1 0ΔNLS and uncover a probable sex bias in the induction of IFN-α/β in the cornea during HSV-1 infection. Our data show that HSV-1 0ΔNLS lacks neurovirulence even in highly immunocompromised mice lacking the IFN-α/β receptor. These studies support the translational viability of the HSV-1 0ΔNLS vaccine strain by demonstrating that, while it is comparable to a virulent parental strain in terms of immunogenicity, HSV-1 0ΔNLS does not induce significant tissue pathology.IMPORTANCE HSV-1 is a common human pathogen associated with a variety of clinical presentations ranging in severity from periodic "cold sores" to lethal encephalitis. Despite the consistent failures of HSV subunit vaccines in clinical trials spanning the past 28 years, opposition to live-attenuated HSV vaccines predicated on unfounded safety concerns currently limits their widespread acceptance. Here, we demonstrate that a live-attenuated HSV-1 vaccine has great translational potential.
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24
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Devault AM, Mortimer TD, Kitchen A, Kiesewetter H, Enk JM, Golding GB, Southon J, Kuch M, Duggan AT, Aylward W, Gardner SN, Allen JE, King AM, Wright G, Kuroda M, Kato K, Briggs DE, Fornaciari G, Holmes EC, Poinar HN, Pepperell CS. A molecular portrait of maternal sepsis from Byzantine Troy. eLife 2017; 6. [PMID: 28072390 PMCID: PMC5224923 DOI: 10.7554/elife.20983] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/24/2016] [Indexed: 12/14/2022] Open
Abstract
Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman’s remains. Scanning electron microscopy of the tissue revealed ‘ghost cells’, resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that G. vaginalis Troy fell within contemporary genetic diversity, whereas S. saprophyticus Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of S. saprophyticus infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections. DOI:http://dx.doi.org/10.7554/eLife.20983.001 Why and how have some bacteria evolved to cause illness in humans? One way to study bacterial evolution is to search for ancient samples of bacteria and use DNA sequencing technology to investigate how modern bacteria have changed from their ancestors. Understanding the evolution process may help researchers to understand how some bacteria become resistant to the antibiotics designed to kill them. Complications that occur during pregnancy, including bacterial infections, have long been a major cause of death for women. Now, Devault, Mortimer et al. have been able to sequence the DNA of bacteria found in tissue collected from a woman buried 800 years ago in a cemetery in Troy. Some of the woman’s tissues had been well preserved because they had calcified (probably as the result of infection), which preserved their structure in a mineralized layer. Two mineralized “nodules” in the body appear to be the remains of abscesses. Some of the human DNA in the nodules came from a male, suggesting that the woman was pregnant with a boy and that the abscesses formed in placental tissue. Sequencing the DNA of the bacteria in the abscess allowed Devault, Mortimer et al. to diagnose the woman’s infection, which was caused by two types of bacteria. One species, called Gardnerella vaginalis, is found in modern pregnancy-related infections. The DNA of the ancient samples was similar to that of modern bacteria. The other bacteria species was an ancient form of Staphylococcus saprophyticus, a type of bacteria that causes urinary tract infections. However, the DNA of the ancient S. saprophyticus bacteria is quite different to that of the bacteria found in modern humans. Instead, their DNA sequence appears more similar to forms of the bacteria that infect currently livestock. As humans lived closely with their livestock at the time the woman lived, her infection may be due to a type of bacteria that passed easily between humans and animals. Overall, the results suggest that the disease-causing properties of bacteria can arise from a wide range of sources. In addition, Devault, Mortimer et al. have demonstrated that certain types of tissue found in archeological remains are a potential gold mine of information about the evolution of bacteria and other microbes found in the human body. DOI:http://dx.doi.org/10.7554/eLife.20983.002
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Affiliation(s)
- Alison M Devault
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,MYcroarray, Ann Arbor, United States
| | - Tatum D Mortimer
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, United States
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, United States
| | - Henrike Kiesewetter
- Project Troia, Institute of Prehistory, Early History, and Medieval Archaeology, Tübingen University, Tübingen, Germany
| | - Jacob M Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,MYcroarray, Ann Arbor, United States
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Canada
| | - John Southon
- Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, United States
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - William Aylward
- Molecular Archaeology Laboratory, Biotechnology Center, University of Wisconsin-Madison, Madison, United States.,Department of Classics and Ancient Near Eastern Studies, University of Wisconsin-Madison, Madison, United States
| | - Shea N Gardner
- Lawrence Livermore National Laboratory, Livermore, United States
| | - Jonathan E Allen
- Lawrence Livermore National Laboratory, Livermore, United States
| | - Andrew M King
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Gerard Wright
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kengo Kato
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Derek Eg Briggs
- Department of Geology and Geophysics, Yale University, New Haven, United States
| | - Gino Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States.,Molecular Archaeology Laboratory, Biotechnology Center, University of Wisconsin-Madison, Madison, United States.,Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
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25
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Pandey U, Bell AS, Renner DW, Kennedy DA, Shreve JT, Cairns CL, Jones MJ, Dunn PA, Read AF, Szpara ML. DNA from Dust: Comparative Genomics of Large DNA Viruses in Field Surveillance Samples. mSphere 2016; 1:e00132-16. [PMID: 27747299 PMCID: PMC5064450 DOI: 10.1128/msphere.00132-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/25/2016] [Indexed: 12/12/2022] Open
Abstract
The intensification of the poultry industry over the last 60 years facilitated the evolution of increased virulence and vaccine breaks in Marek's disease virus (MDV-1). Full-genome sequences are essential for understanding why and how this evolution occurred, but what is known about genome-wide variation in MDV comes from laboratory culture. To rectify this, we developed methods for obtaining high-quality genome sequences directly from field samples without the need for sequence-based enrichment strategies prior to sequencing. We applied this to the first characterization of MDV-1 genomes from the field, without prior culture. These viruses were collected from vaccinated hosts that acquired naturally circulating field strains of MDV-1, in the absence of a disease outbreak. This reflects the current issue afflicting the poultry industry, where virulent field strains continue to circulate despite vaccination and can remain undetected due to the lack of overt disease symptoms. We found that viral genomes from adjacent field sites had high levels of overall DNA identity, and despite strong evidence of purifying selection, had coding variations in proteins associated with virulence and manipulation of host immunity. Our methods empower ecological field surveillance, make it possible to determine the basis of viral virulence and vaccine breaks, and can be used to obtain full genomes from clinical samples of other large DNA viruses, known and unknown. IMPORTANCE Despite both clinical and laboratory data that show increased virulence in field isolates of MDV-1 over the last half century, we do not yet understand the genetic basis of its pathogenicity. Our knowledge of genome-wide variation between strains of this virus comes exclusively from isolates that have been cultured in the laboratory. MDV-1 isolates tend to lose virulence during repeated cycles of replication in the laboratory, raising concerns about the ability of cultured isolates to accurately reflect virus in the field. The ability to directly sequence and compare field isolates of this virus is critical to understanding the genetic basis of rising virulence in the wild. Our approaches remove the prior requirement for cell culture and allow direct measurement of viral genomic variation within and between hosts, over time, and during adaptation to changing conditions.
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Affiliation(s)
- Utsav Pandey
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew S. Bell
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Daniel W. Renner
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - David A. Kennedy
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jacob T. Shreve
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Chris L. Cairns
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Matthew J. Jones
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Patricia A. Dunn
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Moriah L. Szpara
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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Karbalaie Niya MH, Bokharaei Salim F, Tavakoli A, Reza Monavari SH, Esghaei M, Tameshkel FS, Keyvani H. Varicella zoster virus genotyping in chickenpox patient's clinical isolates from Iran. Future Virol 2016. [DOI: 10.2217/fvl-2016-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: The varicella zoster virus (VZV) causes chickenpox and zoster infections. This study aimed to investigate the distribution of VZV genotypes among Iranian patients. Materials & methods: From 2010 to 2015, 244 patients were enrolled in this cross-sectional study, 45 of whom were positive for VZV DNA. Both direct sequencing and restriction fragment length polymorphism assay were performed for 19 positive specimens. SPSS v.20 was used for statistics. Results: The predominant VZV genotype was M1 (84.2%) followed by genotype E (10.5%) and genotype J (5.3%). Restriction fragment length polymorphism demonstrated that 17 strains were PstI+ BglI+ (M1 and/or J genotypes) and 2 were PstI+ BglI- (E genotype). Conclusion: This research is a prelim study on VZV genotyping. Further investigations will help to confirm the VZV genotype prevalence reported here.
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Affiliation(s)
| | | | - Ahmad Tavakoli
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | | | - Maryam Esghaei
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Keyvani
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
- Gastrointestinal & Liver Disease Research Center (GILDRC), Iran University of Medical Sciences, Tehran, Iran
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Safarnezhad Tameshkel F, Karbalaie Niya MH, Keyvani H. Enzymatic Digestion Pattern of Varicella Zoster Virus ORF38 and ORF54 in Chickenpox Patients Using RFLP Technique. IRANIAN JOURNAL OF PATHOLOGY 2016; 11:35-40. [PMID: 26870141 PMCID: PMC4749193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/30/2015] [Indexed: 11/21/2022]
Abstract
BACKGROUND Varicella zoster virus (VZV) causes chickenpox in children and zoster (zona) in the elderly. Using RFLP-PCR method for detection of VZV specific SNPs ORF38, 54 and 62 could distinguish the profile of VZV isolates. The aim of this study was to investigate enzymatic digestion pattern of VZV ORF38 and ORF54 in chickenpox patients using RFLP technique. METHODS Thirty-eight chickenpox patients, who referred to the hospitals of Iran University of Medical Sciences in Tehran from May 2010 to June 2015 were enrolled in this cross sectional study. After the DNA extraction, PCR amplification of 38 VZV isolates performed by specific primers of ORFs 38 and 54, then RFLP assay and digestion carried out by PstI (for ORF38) and BglI (for ORF54) restriction enzymes. RESULTS Of 38 positive VZV DNA, the mean age (yr)±SD was 34.4±23.3 (range: 7-89). 22 (57.9%) were female and 16 (42.1%) were male. The predominant VZV profile of BglI(+) PstI(+) were 89.5% (34/38) followed by 10.5% (4/38) PstI(+) BglI‾. Statistical analysis showed that there was no significant relationship between genotype, age, sex, and year of infection variables (P value> 0.05). The common VZV genotype among Iranian patients with chickenpox and zona infection is genotype BglI(+) PstI(+) followed by PstI(+) BglI‾. CONCLUSION There are different VZV circulating genotypes that call for for more research on this field by widely population and other methods such as nucleotide sequencing to justify the accurate VZV genotype prevalence in Iran.
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Affiliation(s)
| | | | - Hossein Keyvani
- Dept. of Virology, Iran University of Medical Sciences, Tehran, Iran
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