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Smiley Evans T, Lowenstine LJ, Ssebide B, Barry PA, Kinani JF, Nizeyimana F, Noheli JB, Okello R, Mudakikwa A, Cranfield MR, Mazet JAK, Johnson CK, Gilardi KV. Simian homologues of human herpesviruses and implications for novel viral introduction to free-living mountain gorillas. Am J Primatol 2023; 85:e23439. [PMID: 36263518 PMCID: PMC11017921 DOI: 10.1002/ajp.23439] [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: 04/22/2022] [Revised: 08/17/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023]
Abstract
The endangered mountain gorilla (Gorilla beringei beringei) in Rwanda, Uganda, and the Democratic Republic of Congo is frequently in contact with humans through tourism, research activities, and illegal entry of people into protected gorilla habitat. Herpesviruses, which are ubiquitous in primates, have the potential to be shared in any setting where humans and gorillas share habitat. Based on serological findings and clinical observations of orofacial ulcerated lesions resembling herpetic lesions, an alpha-herpesvirus resembling human herpes simplex virus type 1 (HSV-1) has long been suspected to be present in human-habituated mountain gorillas in the wild. While the etiology of orofacial lesions in the wild has not been confirmed, HSV-1 has been suspected in captively-housed mountain gorillas and confirmed in a co-housed confiscated Grauer's gorilla (Gorilla beringei graueri). To better characterize herpesviruses infecting mountain gorillas and to determine the presence/absence of HSV-1 in the free-living population, we conducted a population-wide survey to test for the presence of orally shed herpesviruses. DNA was extracted from discarded chewed plants collected from 294 individuals from 26 groups, and samples were screened by polymerase chain reaction using pan-herpesvirus and HSV-1-specific assays. We found no evidence that human herpesviruses had infected free-ranging mountain gorillas. However, we found gorilla-specific homologs to human herpesviruses, including cytomegaloviruses (GbbCMV-1 and 2), a lymphocryptovirus (GbbLCV-1), and a new rhadinovirus (GbbRHV-1) with similar characteristics (i.e., timing of primary infection, shedding in multiple age groups, and potential modes of transmission) to their human counterparts, human cytomegalovirus, Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, respectively.
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Affiliation(s)
- Tierra Smiley Evans
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Linda J Lowenstine
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Benard Ssebide
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Peter A Barry
- Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, California National Primate Research Center, University of California Davis, Davis, California, USA
| | - Jean Felix Kinani
- One Health Approach for Conservation (OHAC), Gorilla Health, Kigali, Rwanda
| | - Fred Nizeyimana
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Jean Bosco Noheli
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Ricky Okello
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | | | - Michael R Cranfield
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Jonna A K Mazet
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
| | - Christine K Johnson
- Epicenter for Disease Dynamics, One Health Institute, University of California Davis, Davis, California, USA
| | - Kirsten V Gilardi
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, California, USA
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Dunay E, Owens LA, Dunn CD, Rukundo J, Atencia R, Cole MF, Cantwell A, Emery Thompson M, Rosati AG, Goldberg TL. Viruses in sanctuary chimpanzees across Africa. Am J Primatol 2023; 85:e23452. [PMID: 36329642 PMCID: PMC9812903 DOI: 10.1002/ajp.23452] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Infectious disease is a major concern for both wild and captive primate populations. Primate sanctuaries in Africa provide critical protection to thousands of wild-born, orphan primates confiscated from the bushmeat and pet trades. However, uncertainty about the infectious agents these individuals potentially harbor has important implications for their individual care and long-term conservation strategies. We used metagenomic next-generation sequencing to identify viruses in blood samples from chimpanzees (Pan troglodytes) in three sanctuaries in West, Central, and East Africa. Our goal was to evaluate whether viruses of human origin or other "atypical" or unknown viruses might infect these chimpanzees. We identified viruses from eight families: Anelloviridae, Flaviviridae, Genomoviridae, Hepadnaviridae, Parvoviridae, Picobirnaviridae, Picornaviridae, and Rhabdoviridae. The majority (15/26) of viruses identified were members of the family Anelloviridae and represent the genera Alphatorquevirus (torque teno viruses) and Betatorquevirus (torque teno mini viruses), which are common in chimpanzees and apathogenic. Of the remaining 11 viruses, 9 were typical constituents of the chimpanzee virome that have been identified in previous studies and are also thought to be apathogenic. One virus, a novel tibrovirus (Rhabdoviridae: Tibrovirus) is related to Bas-Congo virus, which was originally thought to be a human pathogen but is currently thought to be apathogenic, incidental, and vector-borne. The only virus associated with disease was rhinovirus C (Picornaviridae: Enterovirus) infecting one chimpanzee subsequent to an outbreak of respiratory illness at that sanctuary. Our results suggest that the blood-borne virome of African sanctuary chimpanzees does not differ appreciably from that of their wild counterparts, and that persistent infection with exogenous viruses may be less common than often assumed.
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Affiliation(s)
- Emily Dunay
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christopher D Dunn
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joshua Rukundo
- Ngamba Island Chimpanzee Sanctuary/Chimpanzee Trust, Entebbe, Uganda
| | - Rebeca Atencia
- Jane Goodall Institute Congo, Pointe-Noire, Republic of Congo
| | - Megan F Cole
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Averill Cantwell
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Alexandra G Rosati
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Anthropology, University of Michigan, Ann Arbor, Michigan, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
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3
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Phan QV, Bogdanow B, Wyler E, Landthaler M, Liu F, Hagemeier C, Wiebusch L. Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus. PLoS Pathog 2022; 18:e1010193. [PMID: 34982803 PMCID: PMC8759705 DOI: 10.1371/journal.ppat.1010193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/14/2022] [Accepted: 12/09/2021] [Indexed: 11/19/2022] Open
Abstract
The chimpanzee cytomegalovirus (CCMV) is the closest relative of human CMV (HCMV). Because of the high conservation between these two species and the ability of human cells to fully support CCMV replication, CCMV holds great potential as a model system for HCMV. To make the CCMV genome available for precise and rapid gene manipulation techniques, we captured the genomic DNA of CCMV strain Heberling as a bacterial artificial chromosome (BAC). Selected BAC clones were reconstituted to infectious viruses, growing to similar high titers as parental CCMV. DNA sequencing confirmed the integrity of our clones and led to the identification of two polymorphic loci and a deletion-prone region within the CCMV genome. To re-evaluate the CCMV coding potential, we analyzed the viral transcriptome and proteome and identified several novel ORFs, splice variants, and regulatory RNAs. We further characterized the dynamics of CCMV gene expression and found that viral proteins cluster into five distinct temporal classes. In addition, our datasets revealed that the host response to CCMV infection and the de-regulation of cellular pathways are in line with known hallmarks of HCMV infection. In a first functional experiment, we investigated a proposed frameshift mutation in UL128 that was suspected to restrict CCMV's cell tropism. In fact, repair of this frameshift re-established productive CCMV infection in endothelial and epithelial cells, expanding the options of CCMV as an infection model. Thus, BAC-cloned CCMV can serve as a powerful tool for systematic approaches in comparative functional genomics, exploiting the close phylogenetic relationship between CCMV and HCMV.
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Affiliation(s)
- Quang Vinh Phan
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Boris Bogdanow
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Christian Hagemeier
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Lüder Wiebusch
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Berlin, Germany
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Abstract
Over the last two decades, the viromes of our closest relatives, the African great apes (AGA), have been intensively studied. Comparative approaches have unveiled diverse evolutionary patterns, highlighting both stable host-virus associations over extended evolutionary timescales and much more recent viral emergence events. In this chapter, we summarize these findings and outline how they have shed a new light on the origins and evolution of many human-infecting viruses. We also show how this knowledge can be used to better understand the evolution of human health in relation to viral infections.
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Sebastiano M, Canestrelli D, Bisconti R, Lavergne A, Pineau K, Chastel O, Lacoste V, Costantini D. Detection and Phylogenetic Characterization of a Novel Herpesvirus in Sooty Terns Onychoprion fuscatus. Front Vet Sci 2020; 7:567. [PMID: 33088826 PMCID: PMC7493666 DOI: 10.3389/fvets.2020.00567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/16/2020] [Indexed: 12/19/2022] Open
Abstract
Since 2005, we have recorded annual episodes of alphaherpesvirus outbreaks in chicks of magnificent frigatebird Fregata magnificens on the Ile du Grand Connétable Nature Reserve in French Guiana. In 2009, we found sooty terns, Onychoprion fuscatus, that live sympatrically with frigatebirds, with visible clinical signs of a potential viral infection. To determine if the symptoms observed in sooty terns could be associated with an alphaherpesvirus previously identified in frigatebirds, we carried out molecular screening of samples collected from seven individuals. We identified and characterized a novel viral sequence from five birds. BLAST searches, pairwise nucleotide, and amino acid sequence comparisons, as well as phylogenetic analyses confirmed that the sequence belonged to the Herpesviridae family, of the Alphaherpesvirinae subfamily. We observed that it clustered with strains isolated from Podargidae (Caprimulgiformes), Columbiformes, and Falconiformes, but was distinct from the frigatebird herpesvirus. We have tentatively named it Onychoprion fuscatus alphaherpesvirus 1, (OfusAHV1). These two sequences, although found syntopic on the Ile du Grand Connétable, belong to two distinct alphaherpesvirus strains. Thus, the clinical symptoms showed by sooty terns do not likely result from a cross-species transmission event. Future work is needed to better characterize the virus and to investigate herpesvirus prevalence in healthy, free-ranging sooty terns, and to assess the impact of the virus on population viability.
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Affiliation(s)
- Manrico Sebastiano
- Centre d'Etudes Biologiques de Chizé (CEBC), UMR 7372 CNRS-Univ, La Rochelle, France
| | - Daniele Canestrelli
- Department of Ecological and Biological Science, Tuscia University, Viterbo, Italy
| | - Roberta Bisconti
- Department of Ecological and Biological Science, Tuscia University, Viterbo, Italy
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, France
| | - Kévin Pineau
- Groupe d'Etude et de Protection des Oiseaux en Guyane (GEPOG), Rémire-Montjoly, France
| | - Olivier Chastel
- Centre d'Etudes Biologiques de Chizé (CEBC), UMR 7372 CNRS-Univ, La Rochelle, France
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, France.,Unité de Biologie des Infections Virales Emergentes, Centre International de Recherche en Infectiologie, Institut Pasteur, Lyon, France
| | - David Costantini
- Unité Physiologie moléculaire et adaptation (PhyMA), Muséum National d'Histoire Naturelle, CNRS, CP32, Paris, France
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Winter JR, Jackson C, Lewis JEA, Taylor GS, Thomas OG, Stagg HR. Predictors of Epstein-Barr virus serostatus and implications for vaccine policy: A systematic review of the literature. J Glob Health 2020; 10:010404. [PMID: 32257152 PMCID: PMC7125428 DOI: 10.7189/jogh.10.010404] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV) is an important human pathogen; it infects >90% people globally and is linked to infectious mononucleosis and several types of cancer. Vaccines against EBV are in development. In this study we present the first systematic review of the literature on risk factors for EBV infection, and discuss how they differ between settings, in order to improve our understanding of EBV epidemiology and aid the design of effective vaccination strategies. METHODS MEDLINE, Embase, and Web of Science were searched on 6th March 2017 for observational studies of risk factors for EBV infection. Studies were excluded if they were published before 2008 to ensure relevance to the modern day, given the importance of influencing future vaccination policies. There were no language restrictions. After title, abstract and full text screening, followed by checking the reference lists of included studies to identify further studies, data were extracted into standardised spreadsheets and quality assessed. A narrative synthesis was undertaken. RESULTS Seventy-seven papers met our inclusion criteria, including data from 31 countries. There was consistent evidence that EBV seroprevalence was associated with age, increasing throughout childhood and adolescence and remaining constant thereafter. EBV was generally acquired at younger ages in Asia than Europe/North America. There was also compelling evidence for an association between cytomegalovirus infection and EBV. Additional factors associated with EBV seroprevalence, albeit with less consistent evidence, included ethnicity, socioeconomic status, other chronic viral infections, and genetic variants of HLA and immune response genes. CONCLUSIONS Our study is the first systematic review to draw together the global literature on the risk factors for EBV infection and includes an evaluation of the quality of the published evidence. Across the literature, the factors examined are diverse. In Asia, early vaccination of infants would be required to prevent EBV infection. In contrast, in Western countries a vaccine could be deployed later, particularly if it has only a short duration of protection and the intention was to protect against infectious mononucleosis. There is a lack of high-quality data on the prevalence and age of EBV infection outside of Europe, North America and South-East Asia, which are essential for informing effective vaccination policies in these settings.
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Affiliation(s)
- Joanne R Winter
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, London, UK
| | - Charlotte Jackson
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, London, UK
- MRC Clinical Trials Unit, University College London, London, UK
| | - Joanna EA Lewis
- National Institute for Health Research (NIHR) Health Protection Research Unit in Modelling Methodology and Medical Research Council Centre for Outbreak Analysis and Public Health, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Contributed equally and listed alphabetically
| | - Graham S Taylor
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Contributed equally and listed alphabetically
| | - Olivia G Thomas
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Helen R Stagg
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, London, UK
- Usher Institute, University of Edinburgh, Edinburgh, UK
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Cagliani R, Forni D, Mozzi A, Sironi M. Evolution and Genetic Diversity of Primate Cytomegaloviruses. Microorganisms 2020; 8:E624. [PMID: 32344906 PMCID: PMC7285053 DOI: 10.3390/microorganisms8050624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 12/30/2022] Open
Abstract
Cytomegaloviruses (CMVs) infect many mammals, including humans and non-human primates (NHPs). Human cytomegalovirus (HCMV) is an important opportunistic pathogen among immunocompromised patients and represents the most common infectious cause of birth defects. HCMV possesses a large genome and very high genetic diversity. NHP-infecting CMVs share with HCMV a similar genomic organization and coding content, as well as the course of viral infection. Recent technological advances have allowed the sequencing of several HCMV strains from clinical samples and provided insight into the diversity of NHP-infecting CMVs. The emerging picture indicates that, with the exclusion of core genes (genes that have orthologs in all herpesviruses), CMV genomes are relatively plastic and diverse in terms of gene content, both at the inter- and at the intra-species level. Such variability most likely underlies the strict species-specificity of these viruses, as well as their ability to persist lifelong and with relatively little damage to their hosts. However, core genes, despite their strong conservation, also represented a target of adaptive evolution and subtle changes in their coding sequence contributed to CMV adaptation to different hosts. Indubitably, important knowledge gaps remain, the most relevant of which concerns the role of viral genetics in HCMV-associated human disease.
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Affiliation(s)
| | | | | | - Manuela Sironi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
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Abstract
While non-human primate studies have long been conducted in laboratories, and more recently at zoological parks, sanctuaries are increasingly considered a viable setting for research. Accredited sanctuaries in non-range countries house thousands of primates formerly used as subjects of medical research, trained performers or personal pets. In range countries, however, sanctuaries typically house orphaned primates confiscated from illegal poaching and the bushmeat and pet trafficking trades. Although the primary mission of these sanctuaries is to rescue and rehabilitate residents, many of these organizations are increasingly willing to participate in non-invasive research. Notably, from a scientific standpoint, most sanctuaries provide potential advantages over traditional settings, such as large, naturalistic physical and social environments which may result in more relevant models of primates' free-ranging wild counterparts than other captive settings. As a result, an impressive scope of research in the fields of primate behaviour, cognition, veterinary science, genetics and physiology have been studied in sanctuaries. In this review, we examine the range and form of research that has been conducted at accredited sanctuaries around the world. We also describe the potential challenges of sanctuary-based work and the considerations that external researchers may face when deciding to collaborate with primate sanctuaries on their research projects.
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Affiliation(s)
- Stephen R Ross
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, 2001 North Clark St., Chicago, IL 60614, USA
| | - Jesse G Leinwand
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, 2001 North Clark St., Chicago, IL 60614, USA
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9
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Caposio P, van den Worm S, Crawford L, Perez W, Kreklywich C, Gilbride RM, Hughes CM, Ventura AB, Ratts R, Marshall EE, Malouli D, Axthelm MK, Streblow D, Nelson JA, Picker LJ, Hansen SG, Früh K. Characterization of a live-attenuated HCMV-based vaccine platform. Sci Rep 2019; 9:19236. [PMID: 31848362 PMCID: PMC6917771 DOI: 10.1038/s41598-019-55508-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
Vaccines based on cytomegalovirus (CMV) demonstrate protection in animal models of infectious disease and cancer. Vaccine efficacy is associated with the ability of CMV to elicit and indefinitely maintain high frequencies of circulating effector memory T cells (TEM) providing continuous, life-long anti-pathogen immune activity. To allow for the clinical testing of human CMV (HCMV)-based vaccines we constructed and characterized as a vector backbone the recombinant molecular clone TR3 representing a wildtype genome. We demonstrate that TR3 can be stably propagated in vitro and that, despite species incompatibility, recombinant TR3 vectors elicit high frequencies of TEM to inserted antigens in rhesus macaques (RM). Live-attenuated versions of TR3 were generated by deleting viral genes required to counteract intrinsic and innate immune responses. In addition, we eliminated subunits of a viral pentameric glycoprotein complex thus limiting cell tropism. We show in a humanized mouse model that such modified vectors were able to establish persistent infection but lost their ability to reactivate from latency. Nevertheless, attenuated TR3 vectors preserved the ability to elicit and maintain TEM to inserted antigens in RM. We further demonstrate that attenuated TR3 can be grown in approved cell lines upon elimination of an anti-viral host factor using small interfering RNA, thus obviating the need for a complementing cell line. In sum, we have established a versatile platform for the clinical development of live attenuated HCMV-vectored vaccines and immunotherapies.
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Affiliation(s)
- Patrizia Caposio
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Sjoerd van den Worm
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
- Batavia Biosciences B.V., Zernikedreef 16, 2333 CL, Leiden, Netherlands
| | - Lindsey Crawford
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Wilma Perez
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Craig Kreklywich
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Roxanne M Gilbride
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Robert Ratts
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
- Vir Biotechnology, 4640, SW Macadam Avenue, Portland, OR, 97239, USA
| | - Emily E Marshall
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
- Vir Biotechnology, 4640, SW Macadam Avenue, Portland, OR, 97239, USA
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Daniel Streblow
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Jay A Nelson
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA.
| | - Klaus Früh
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, 97006, USA.
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10
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Murthy S, O'Brien K, Agbor A, Angedakin S, Arandjelovic M, Ayimisin EA, Bailey E, Bergl RA, Brazzola G, Dieguez P, Eno-Nku M, Eshuis H, Fruth B, Gillespie TR, Ginath Y, Gray M, Herbinger I, Jones S, Kehoe L, Kühl H, Kujirakwinja D, Lee K, Madinda NF, Mitamba G, Muhindo E, Nishuli R, Ormsby LJ, Petrzelkova KJ, Plumptre AJ, Robbins MM, Sommer V, Ter Heegde M, Todd A, Tokunda R, Wessling E, Jarvis MA, Leendertz FH, Ehlers B, Calvignac-Spencer S. Cytomegalovirus distribution and evolution in hominines. Virus Evol 2019; 5:vez015. [PMID: 31384482 PMCID: PMC6671425 DOI: 10.1093/ve/vez015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Herpesviruses are thought to have evolved in very close association with their hosts. This is notably the case for cytomegaloviruses (CMVs; genus Cytomegalovirus) infecting primates, which exhibit a strong signal of co-divergence with their hosts. Some herpesviruses are however known to have crossed species barriers. Based on a limited sampling of CMV diversity in the hominine (African great ape and human) lineage, we hypothesized that chimpanzees and gorillas might have mutually exchanged CMVs in the past. Here, we performed a comprehensive molecular screening of all 9 African great ape species/subspecies, using 675 fecal samples collected from wild animals. We identified CMVs in eight species/subspecies, notably generating the first CMV sequences from bonobos. We used this extended dataset to test competing hypotheses with various degrees of co-divergence/number of host switches while simultaneously estimating the dates of these events in a Bayesian framework. The model best supported by the data involved the transmission of a gorilla CMV to the panine (chimpanzee and bonobo) lineage and the transmission of a panine CMV to the gorilla lineage prior to the divergence of chimpanzees and bonobos, more than 800,000 years ago. Panine CMVs then co-diverged with their hosts. These results add to a growing body of evidence suggesting that viruses with a double-stranded DNA genome (including other herpesviruses, adenoviruses, and papillomaviruses) often jumped between hominine lineages over the last few million years.
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Affiliation(s)
- Sripriya Murthy
- Division 12 "Measles, Mumps, Rubella and Viruses Affecting Immune-Compromised Patients" Robert Koch Institute, Berlin, Germany
| | - Kathryn O'Brien
- School of Biomedical and Healthcare Sciences, University of Plymouth, Devon, UK
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,African Parks Network, Lonehill, Republic of South Africa
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | | | - Emma Bailey
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | | | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | | | - Henk Eshuis
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Barbara Fruth
- Faculty of Science, School of Natural Sciences and hPsychology, Liverpool John Moores University, Liverpool, UK.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Thomas R Gillespie
- Department of Environmental Sciences and Program in Population Biology, Ecology, and Evolutionary Biology, Emory University, Atlanta, USA
| | - Yisa Ginath
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Maryke Gray
- International Gorilla Conservation Programme, Kigali, Rwanda.,Batavia Coast Maritime Institute, Geraldton, WA, Australia
| | | | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,Royal Holloway, University of London, Egham, UK
| | - Laura Kehoe
- Wild Chimpanzee Foundation (WCF), Leipzig, Germany.,Department of Biology, University of Victoria, Victoria, Canada.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Hjalmar Kühl
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | | | - Kevin Lee
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,School of Human Evolution and Social Change, Arizona State University, Tempe, USA
| | - Nadège F Madinda
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
| | | | | | - Radar Nishuli
- Réserve de Faune à Okapis, Institut Congolais pour la Conservation de la Nature, Kinshasa, Democratic Republic of the Congo
| | - Lucy J Ormsby
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, Academy of Sciences, Brno, Czech Republic.,Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.,Biology Centre, Institute of Parasitology, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic.,Liberec Zoo, Liberec, Czech Republic
| | - Andrew J Plumptre
- Wildlife Conservation Society, NY, USA.,KBA Secretariat, c/o BirdLife International, Cambridge, UK.,Zoology Department, Conservation Science Group, University of Cambridge, Cambridge, UK
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Volker Sommer
- Gashaka Primate Project, Nigeria c/o Department of Anthropology, University College London, London, UK
| | - Martijn Ter Heegde
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
| | - Angelique Todd
- Dzanga Sangha Protected Areas, WWF Central African Republic, Bangui, Central African Republic
| | - Raymond Tokunda
- Institute of Vertebrate Biology, Academy of Sciences, Brno, Czech Republic
| | - Erin Wessling
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,Dzanga Sangha Protected Areas, WWF Central African Republic, Bangui, Central African Republic
| | - Michael A Jarvis
- School of Biomedical and Healthcare Sciences, University of Plymouth, Devon, UK
| | - Fabian H Leendertz
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
| | - Bernhard Ehlers
- Division 12 "Measles, Mumps, Rubella and Viruses Affecting Immune-Compromised Patients" Robert Koch Institute, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany.,Viral Evolution, Robert Koch Institute, Berlin, Germany
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11
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Goscé L, Winter JR, Taylor GS, Lewis JEA, Stagg HR. Modelling the dynamics of EBV transmission to inform a vaccine target product profile and future vaccination strategy. Sci Rep 2019; 9:9290. [PMID: 31243321 PMCID: PMC6594949 DOI: 10.1038/s41598-019-45381-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/04/2019] [Indexed: 01/06/2023] Open
Abstract
Epstein-Barr virus (EBV) is one of the most common human viruses and the cause of pathologies such as infectious mononucleosis (IM) and certain cancers. No vaccine against EBV infection currently exists, but such vaccines are in development. Knowledge of how EBV is transmitted at the population level is critical to the development of target product profiles (TPPs) for such vaccines and future vaccination strategies. We present the first mathematical model of EBV transmission, parameterised using data from England, and use it to compare hypothetical prophylactic vaccines with different characteristics and the impact of vaccinating different age groups. We found that vaccine duration had more impact than vaccine efficacy on modelled EBV and IM prevalence. The age group vaccinated also had an important effect: vaccinating at a younger age led to a greater reduction in seroprevalence but an increase in IM cases associated with delayed infection. Vaccination had impact on cancer incidence only in the long run, because in England most EBV-related cancers arise in later life. Durability of protection should be a key factor to prioritise in EBV vaccine development and included in vaccine TPPs. These findings are timely and important for vaccine developers and policy-makers alike.
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Affiliation(s)
- Lara Goscé
- University College London, Institute for Global Health, London, WC1N 1EH, UK.
| | - Joanne R Winter
- University College London, Institute for Global Health, London, WC1N 1EH, UK
| | - Graham S Taylor
- University of Birmingham, Institute of Immunology and Immunotherapy, Birmingham, B15 2TT, UK
| | - Joanna E A Lewis
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, School of Public Health, London, W2 1NY, UK
| | - Helen R Stagg
- University College London, Institute for Global Health, London, WC1N 1EH, UK
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, UK
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12
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Willis EL, Stevens TL, White GL, Mcfarlane D. Characterization of Baboon Cytomegalovirus Infection in Healthy Adult Baboons ( Papio anubis). Comp Med 2019; 69:55-62. [PMID: 30704552 DOI: 10.30802/aalas-cm-18-000050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cytomegalovirus (CMV) is a common chronic herpesvirus found in humans and numerous other mammalian species. In people, chronic viruses like CMV can alter overall health and immunity and pose a serious risk for those with an inadequate immune system. In addition, CMV plays an important role in animal health, and could affect the health of vulnerable populations, like endangered species. Previous studies found a high rate of CMV seropositivity among adult baboons (Papio anubis), and results from our laboratory revealed that baboon CMV (BaCMV) seropositivity was correlated with altered immune cell populations. In the current study, we further characterized BaCMV infection in normal, adult baboons. Analysis of blood samples from baboons (age, 6 to 26 y) revealed a low overall prevalence of detectable of BaCMV DNA, with a higher detection rate in aged baboons (older than 15 y). Furthermore, data suggest that individual baboons maintain similar rates of recurrence and levels of BaCMV shedding in saliva over time. Finally, we evaluated multiple commercially available assays for antihuman CMV IgG and IgM for use with baboon sera. Results of this study will improve our understanding of BaCMV and may be directly relevant to other closely related species.
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Affiliation(s)
- Erin L Willis
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma
| | - Taylor L Stevens
- Department of Comparative Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Gary L White
- Department of Comparative Medicine, Primate Consulting, Edmond, Oklahoma
| | - Dianne Mcfarlane
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma;,
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13
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DNA Polymerase Sequences of New World Monkey Cytomegaloviruses: Another Molecular Marker with Which To Infer Platyrrhini Systematics. J Virol 2018; 92:JVI.00980-18. [PMID: 29976674 DOI: 10.1128/jvi.00980-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/27/2018] [Indexed: 01/22/2023] Open
Abstract
Over the past few decades, a large number of studies have identified herpesvirus sequences from many mammalian species around the world. Among the different nonhuman primate species tested so far for cytomegaloviruses (CMVs), only a few were from the New World. Seeking to identify CMV homologues in New World monkeys (NWMs), we carried out molecular screening of 244 blood DNA samples from 20 NWM species from Central and South America. Our aim was to reach a better understanding of their evolutionary processes within the Platyrrhini parvorder. Using PCR amplification with degenerate consensus primers targeting highly conserved amino acid motifs encoded by the herpesvirus DNA polymerase gene, we characterized novel viral sequences from 12 species belonging to seven genera representative of the three NWM families. BLAST searches, pairwise nucleotide and amino acid sequence comparisons, and phylogenetic analyses confirmed that they all belonged to the Cytomegalovirus genus. Previously determined host taxa allowed us to demonstrate a good correlation between the distinct monophyletic clades of viruses and those of the infected primates at the genus level. In addition, the evolutionary branching points that separate NWM CMVs were congruent with the divergence dates of their hosts at the genus level. These results significantly expand our knowledge of the host range of this viral genus and strongly support the occurrence of cospeciation between these viruses and their hosts. In this respect, we propose that NWM CMV DNA polymerase gene sequences may serve as reliable molecular markers with which to infer Platyrrhini phylogenetics.IMPORTANCE Investigating evolutionary processes between viruses and nonhuman primates has led to the discovery of a large number of herpesviruses. No study published so far on primate cytomegaloviruses has extensively studied New World monkeys (NWMs) at the subspecies, species, genus, and family levels. The present study sought to identify cytomegalovirus homologues in NWMs and to decipher their evolutionary relationships. This led us to characterize novel viruses from 12 of the 20 primate species tested, which are representative of the three NWM families. The identification of distinct viruses in these primates not only significantly expands our knowledge of the host range of this viral genus but also sheds light on its evolutionary history. Phylogenetic analyses and molecular dating of the sequences obtained support a virus-host coevolution.
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14
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Lowenstine LJ, McManamon R, Terio KA. Apes. PATHOLOGY OF WILDLIFE AND ZOO ANIMALS 2018. [PMCID: PMC7173580 DOI: 10.1016/b978-0-12-805306-5.00015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Cytomegaloviruses in a Community of Wild Nonhuman Primates in Taï National Park, Côte D'Ivoire. Viruses 2017; 10:v10010011. [PMID: 29286318 PMCID: PMC5795424 DOI: 10.3390/v10010011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/01/2022] Open
Abstract
Cytomegaloviruses (CMVs) are known to infect many mammals, including a number of nonhuman primates (NHPs). However, most data available arose from studies led on captive individuals and little is known about CMV diversity in wild NHPs. Here, we analyzed a community of wild nonhuman primates (seven species) in Taï National Park (TNP), Côte d’Ivoire, with two PCR systems targeting betaherpesviruses. CMV DNA was detected in 17/87 primates (4/7 species). Six novel CMVs were identified in sooty mangabeys, Campbell’s monkeys and Diana monkeys, respectively. In 3/17 positive individuals (from three NHP species), different CMVs were co-detected. A major part of the glycoprotein B coding sequences of the novel viruses was amplified and sequenced, and phylogenetic analyses were performed that included three previously discovered CMVs of western red colobus from TNP and published CMVs from other NHP species and geographic locations. We find that, despite this locally intensified sampling, NHP CMVs from TNP are completely host-specific, pinpointing the absence or rarity of cross-species transmission. We also show that on longer timescales the evolution of CMVs is characterized by frequent co-divergence with their hosts, although other processes, including lineage duplication and host switching, also have to be invoked to fully explain their evolutionary relationships.
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16
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Pozo F, Juste J, Vázquez-Morón S, Aznar-López C, Ibáñez C, Garin I, Aihartza J, Casas I, Tenorio A, Echevarría JE. Identification of Novel Betaherpesviruses in Iberian Bats Reveals Parallel Evolution. PLoS One 2016; 11:e0169153. [PMID: 28036408 PMCID: PMC5201282 DOI: 10.1371/journal.pone.0169153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022] Open
Abstract
A thorough search for bat herpesviruses was carried out in oropharyngeal samples taken from most of the bat species present in the Iberian Peninsula from the Vespertilionidae, Miniopteridae, Molossidae and Rhinolophidae families, in addition to a colony of captive fruit bats from the Pteropodidae family. By using two degenerate consensus PCR methods targeting two conserved genes, distinct and previously unrecognized bat-hosted herpesviruses were identified for the most of the tested species. All together a total of 42 potentially novel bat herpesviruses were partially characterized. Thirty-two of them were tentatively assigned to the Betaherpesvirinae subfamily while the remaining 10 were allocated into the Gammaherpesvirinae subfamily. Significant diversity was observed among the novel sequences when compared with type herpesvirus species of the ICTV-approved genera. The inferred phylogenetic relationships showed that most of the betaherpesviruses sequences fell into a well-supported unique monophyletic clade and support the recognition of a new betaherpesvirus genus. This clade is subdivided into three major clades, corresponding to the families of bats studied. This supports the hypothesis of a species-specific parallel evolution process between the potentially new betaherpesviruses and their bat hosts. Interestingly, two of the betaherpesviruses’ sequences detected in rhinolophid bats clustered together apart from the rest, closely related to viruses that belong to the Roseolovirus genus. This suggests a putative third roseolo lineage. On the contrary, no phylogenetic structure was detected among several potentially novel bat-hosted gammaherpesviruses found in the study. Remarkably, all of the possible novel bat herpesviruses described in this study are linked to a unique bat species.
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Affiliation(s)
- Francisco Pozo
- Virology Section, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Javier Juste
- Estación Biológica de Doñana, CSIC, Seville, Spain
| | - Sonia Vázquez-Morón
- Virology Section, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Carolina Aznar-López
- Virology Section, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | - Inazio Garin
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Leioa, The Basque Country, Spain
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Leioa, The Basque Country, Spain
| | - Inmaculada Casas
- Virology Section, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Antonio Tenorio
- Virology Section, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Juan Emilio Echevarría
- Virology Section, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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17
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Bats, Primates, and the Evolutionary Origins and Diversification of Mammalian Gammaherpesviruses. mBio 2016; 7:mBio.01425-16. [PMID: 27834200 PMCID: PMC5101351 DOI: 10.1128/mbio.01425-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Gammaherpesviruses (γHVs) are generally considered host specific and to have codiverged with their hosts over millions of years. This tenet is challenged here by broad-scale phylogenetic analysis of two viral genes using the largest sample of mammalian γHVs to date, integrating for the first time bat γHV sequences available from public repositories and newly generated viral sequences from two vampire bat species (Desmodus rotundus and Diphylla ecaudata). Bat and primate viruses frequently represented deep branches within the supported phylogenies and clustered among viruses from distantly related mammalian taxa. Following evolutionary scenario testing, we determined the number of host-switching and cospeciation events. Cross-species transmissions have occurred much more frequently than previously estimated, and most of the transmissions were attributable to bats and primates. We conclude that the evolution of the Gammaherpesvirinae subfamily has been driven by both cross-species transmissions and subsequent cospeciation within specific viral lineages and that the bat and primate orders may have potentially acted as superspreaders to other mammalian taxa throughout evolutionary history. It has long been believed that herpesviruses have coevolved with their hosts and are species specific. Nevertheless, a global evolutionary analysis of bat viruses in the context of other mammalian viruses, which could put this widely accepted view to the test, had not been undertaken until now. We present two main findings that may challenge the current view of γHV evolution: multiple host-switching events were observed at a higher rate than previously appreciated, and bats and primates harbor a large diversity of γHVs which may have led to increased cross-species transmissions from these taxa to other mammals.
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18
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Russell JNH, Marsh AK, Willer DO, Ambagala APN, Dzamba M, Chan JK, Pilon R, Fournier J, Brudno M, Antony JM, Sandstrom P, Evans BJ, MacDonald KS. A novel strain of cynomolgus macaque cytomegalovirus: implications for host-virus co-evolution. BMC Genomics 2016; 17:277. [PMID: 27044312 PMCID: PMC4820910 DOI: 10.1186/s12864-016-2588-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/14/2016] [Indexed: 12/20/2022] Open
Abstract
Background Cytomegaloviruses belong to a large, ancient, genus of DNA viruses comprised of a wide array of species-specific strains that occur in diverse array of hosts. Methods In this study we sequenced the ~217 Kb genome of a cytomegalovirus isolated from a Mauritius cynomolgus macaque, CyCMV Mauritius, and compared it to previously sequenced cytomegaloviruses from a cynomolgus macaque of Filipino origin (CyCMV Ottawa) and two from Indian rhesus macaques (RhCMV 180.92 and RhCMV 68–1). Results Though more closely related to CyCMV Ottawa, CyCMV Mauritius is less genetically distant from both RhCMV strains than is CyCMV Ottawa. Several individual genes, including homologues of CMV genes RL11B, UL123, UL83b, UL84 and a homologue of mammalian COX-2, show a closer relationship between homologues of CyCMV Mauritius and the RhCMVs than between homologues of CyCMV Mauritius and CyCMV Ottawa. A broader phylogenetic analysis of 12 CMV strains from eight species recovers evolutionary relationships among viral strains that mirror those amongst the host species, further demonstrating co-evolution of host and virus. Conclusions Phylogenetic analyses of rhesus and cynomolgus macaque CMV genome sequences demonstrate co-speciation of the virus and host. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2588-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Angie K Marsh
- Department of Immunology, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - David O Willer
- Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Aruna P N Ambagala
- Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.,Present Address: Canadian Science Centre for Human and Animal Health, National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, R3E 3M4, MB, Canada
| | - Misko Dzamba
- Department of Computer Science, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Jacqueline K Chan
- Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Richard Pilon
- National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, K1A 0K9, ON, Canada
| | - Jocelyn Fournier
- Scientific Services Division, Health Products & Food Branch, Health Canada, Ottawa, K1A 0L2, ON, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Joseph M Antony
- Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada
| | - Paul Sandstrom
- National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, K1A 0K9, ON, Canada
| | - Ben J Evans
- Biology Department, McMaster University, Life Sciences Building, 1280 Main Street West, Hamilton, L8S 4K1, ON, Canada
| | - Kelly S MacDonald
- Department of Immunology, University of Toronto, Toronto, M5S 1A8, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada. .,Department of Microbiology, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada. .,Section of Infectious Diseases, Department of Internal Medicine, University of Manitoba, 745 Bannatyne Ave, Winnipeg, R3E 0J9, MB, Canada. .,Present Address: University of Manitoba, Basic Medical Sciences Building, Room 501, 745 Bannatyne Ave., Winnipeg, R3E 0J9, MB, Canada.
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19
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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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20
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Anoh AE, Akoua-Koffi C, Couacy-Hymann E, Pauly M, Schubert G, Mossoun A, Weiss S, Leendertz SAJ, Jarvis MA, Leendertz FH, Ehlers B. Genetic identification of cytomegaloviruses in a rural population of Côte d'Ivoire. Virol J 2015; 12:155. [PMID: 26437859 PMCID: PMC4594925 DOI: 10.1186/s12985-015-0394-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/24/2015] [Indexed: 01/10/2023] Open
Abstract
Background Cytomegaloviruses (CMVs) are herpesviruses that infect many mammalian species, including humans. Infection generally passes undetected, but the virus can cause serious disease in individuals with impaired immune function. Human CMV (HCMV) is circulating with high seroprevalence (60–100 %) on all continents. However, little information is available on HCMV genoprevalence and genetic diversity in subsaharan Africa, especially in rural areas of West Africa that are at high risk of human-to-human HCMV transmission. In addition, there is a potential for zoonotic spillover of pathogens through bushmeat hunting and handling in these areas as shown for various retroviruses. Although HCMV and nonhuman CMVs are regarded as species-specific, potential human infection with CMVs of non-human primate (NHP) origin, shown to circulate in the local NHP population, has not been studied. Findings Analysis of 657 human oral swabs and fecal samples collected from 518 individuals living in 8 villages of Côte d’Ivoire with generic PCR for identification of human and NHP CMVs revealed shedding of HCMV in 2.5 % of the individuals. Determination of glycoprotein B sequences showed identity with strains Towne, AD169 and Toledo, respectively. NHP CMV sequences were not detected. Conclusions HCMV is actively circulating in a proportion of the rural Côte d’Ivoire human population with circulating strains being closely related to those previously identified in non-African countries. The lack of NHP CMVs in human populations in an environment conducive to cross-species infection supports zoonotic transmission of CMVs to humans being at most a rare event.
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Affiliation(s)
- Augustin Etile Anoh
- Centre de Recherche pour le Développement, Université Alassane Ouattara de Bouake, 01 BP V18, Bouake, Côte d'Ivoire.
| | - Chantal Akoua-Koffi
- Centre de Recherche pour le Développement, Université Alassane Ouattara de Bouake, 01 BP V18, Bouake, Côte d'Ivoire.
| | | | - Maude Pauly
- Project group P3 "Epidemiology of Highly Pathogenic Microorganisms", Robert Koch Institute, Berlin, 13353, Germany. .,Division 12 "Measles, Mumps, Rubella and Viruses affecting immune-compromised patients", Robert Koch Institute, Berlin, 13353, Germany. .,Present address: Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, 4354, Luxembourg.
| | - Grit Schubert
- Project group P3 "Epidemiology of Highly Pathogenic Microorganisms", Robert Koch Institute, Berlin, 13353, Germany.
| | - Arsène Mossoun
- LANADA/Laboratoire Central de Pathologie Animale, Bingerville, 206, Côte d'Ivoire. .,UFR Biosciences, Université FHB, Abidjan-Cocody, Côte d'Ivoire, Abidjan, Côte d'Ivoire.
| | - Sabrina Weiss
- Project group P3 "Epidemiology of Highly Pathogenic Microorganisms", Robert Koch Institute, Berlin, 13353, Germany. .,Present address: European Public Health Microbiology (EUPHEM) training programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden, and Public Health England (PHE), London, NW9 5EQ, UK.
| | - Siv Aina J Leendertz
- Project group P3 "Epidemiology of Highly Pathogenic Microorganisms", Robert Koch Institute, Berlin, 13353, Germany.
| | - Michael A Jarvis
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, United Kingdom.
| | - Fabian H Leendertz
- Project group P3 "Epidemiology of Highly Pathogenic Microorganisms", Robert Koch Institute, Berlin, 13353, Germany.
| | - Bernhard Ehlers
- Division 12 "Measles, Mumps, Rubella and Viruses affecting immune-compromised patients", Robert Koch Institute, Berlin, 13353, Germany.
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Seimon TA, Olson SH, Lee KJ, Rosen G, Ondzie A, Cameron K, Reed P, Anthony SJ, Joly DO, McAloose D, Lipkin WI. Adenovirus and herpesvirus diversity in free-ranging great apes in the Sangha region of the Republic Of Congo. PLoS One 2015; 10:e0118543. [PMID: 25781992 PMCID: PMC4362762 DOI: 10.1371/journal.pone.0118543] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/20/2015] [Indexed: 12/30/2022] Open
Abstract
Infectious diseases have caused die-offs in both free-ranging gorillas and chimpanzees. Understanding pathogen diversity and disease ecology is therefore critical for conserving these endangered animals. To determine viral diversity in free-ranging, non-habituated gorillas and chimpanzees in the Republic of Congo, genetic testing was performed on great-ape fecal samples collected near Odzala-Kokoua National Park. Samples were analyzed to determine ape species, identify individuals in the population, and to test for the presence of herpesviruses, adenoviruses, poxviruses, bocaviruses, flaviviruses, paramyxoviruses, coronaviruses, filoviruses, and simian immunodeficiency virus (SIV). We identified 19 DNA viruses representing two viral families, Herpesviridae and Adenoviridae, of which three herpesviruses had not been previously described. Co-detections of multiple herpesviruses and/or adenoviruses were present in both gorillas and chimpanzees. Cytomegalovirus (CMV) and lymphocryptovirus (LCV) were found primarily in the context of co-association with each other and adenoviruses. Using viral discovery curves for herpesviruses and adenoviruses, the total viral richness in the sample population of gorillas and chimpanzees was estimated to be a minimum of 23 viruses, corresponding to a detection rate of 83%. These findings represent the first description of DNA viral diversity in feces from free-ranging gorillas and chimpanzees in or near the Odzala-Kokoua National Park and form a basis for understanding the types of viruses circulating among great apes in this region.
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Affiliation(s)
- Tracie A. Seimon
- Zoological Health Program, Wildlife Conservation Society, Bronx, New York, United States of America
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | - Sarah H. Olson
- Wildlife Health and Health Policy Program, Wildlife Conservation Society, Bronx, New York, United States of America
- Center for Sustainability and the Global Environment, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kerry Jo Lee
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | - Gail Rosen
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | - Alain Ondzie
- Wildlife Health and Health Policy Program, Wildlife Conservation Society, Bronx, New York, United States of America
| | - Kenneth Cameron
- Wildlife Health and Health Policy Program, Wildlife Conservation Society, Bronx, New York, United States of America
| | - Patricia Reed
- Wildlife Health and Health Policy Program, Wildlife Conservation Society, Bronx, New York, United States of America
| | - Simon J. Anthony
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
| | - Damien O. Joly
- Wildlife Health and Health Policy Program, Wildlife Conservation Society, Bronx, New York, United States of America
| | - Denise McAloose
- Zoological Health Program, Wildlife Conservation Society, Bronx, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, New York, United States of America
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McManus KF, Kelley JL, Song S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Ape Genome Project G, Kidd JM, Wall JD, Bustamante CD, Hammer MF. Inference of gorilla demographic and selective history from whole-genome sequence data. Mol Biol Evol 2014; 32:600-12. [PMID: 25534031 PMCID: PMC4327160 DOI: 10.1093/molbev/msu394] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.
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Affiliation(s)
- Kimberly F McManus
- Department of Biology, Stanford University Department of Biomedical Informatics, Stanford University
| | - Joanna L Kelley
- Department of Genetics, Stanford University School of Biological Sciences, Washington State University
| | - Shiya Song
- Department of Computational Medicine & Bioinformatics, University of Michigan
| | | | | | - Laurie S Stevison
- Institute for Human Genetics, University of California San Francisco
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | | | - Jeffrey M Kidd
- Department of Computational Medicine & Bioinformatics, University of Michigan Department of Human Genetics, University of Michigan
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California San Francisco
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Comparative genome analysis of four elephant endotheliotropic herpesviruses, EEHV3, EEHV4, EEHV5, and EEHV6, from cases of hemorrhagic disease or viremia. J Virol 2014; 88:13547-69. [PMID: 25231309 DOI: 10.1128/jvi.01675-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The genomes of three types of novel endotheliotropic herpesviruses (elephant endotheliotropic herpesvirus 1A [EEHV1A], EEHV1B, and EEHV2) associated with lethal hemorrhagic disease in Asian elephants have been previously well characterized and assigned to a new Proboscivirus genus. Here we have generated 112 kb of DNA sequence data from segments of four more types of EEHV by direct targeted PCR from blood samples or necropsy tissue samples from six viremic elephants. Comparative phylogenetic analysis of nearly 30 protein-encoding genes of EEHV5 and EEHV6 show that they diverge uniformly by nearly 20% from their closest relatives, EEHV2 and EEHV1A, respectively, and are likely to have similar overall gene content and genome organization. In contrast, seven EEHV3 and EEHV4 genes analyzed differ from those of all other EEHVs by 37% and have a G+C content of 63% compared to just 42% for the others. Three strains of EEHV5 analyzed clustered into two partially chimeric subgroups EEHV5A and EEHV5B that diverge by 19% within three small noncontiguous segments totaling 6.2 kb. We conclude that all six EEHV types should be designated as independent species within a proposed new fourth Deltaherpesvirinae subfamily of mammalian herpesviruses. These virus types likely initially diverged close to 100 million years ago when the ancestors of modern elephants split from all other placental mammals and then evolved into two major branches with high- or low-G+C content about 35 million years ago. Later additional branching events subsequently generated three paired sister taxon lineages of which EEHV1 plus EEHV6, EEHV5 plus EEHV2, and EEHV4 plus EEHV3 may represent Asian and African elephant versions, respectively. IMPORTANCE One of the factors threatening the long-term survival of endangered Asian elephants in both wild range countries and in captive breeding populations in zoos is a highly lethal hemorrhagic herpesvirus disease that has killed at least 70 young Asian elephants worldwide. The genomes of the first three types of EEHVs (or probosciviruses) identified have been partially characterized in the preceding accompanying paper (L. K. Richman, J.-C. Zong, E. M. Latimer, J. Lock, R. C. Fleischer, S. Y. Heaggans, and G. S. Hayward, J. Virol. 88:13523-13546, 2014, http://dx.doi.org/10.1128/JVI.01673-14). Here we have used PCR DNA sequence analysis from multiple segments of DNA amplified directly from blood or necropsy tissue samples of six more selected cases of hemorrhagic disease to partially characterize four other types of EEHVs from either Asian or African elephants. We propose that all six types and two chimeric subtypes of EEHV belong to multiple lineages of both AT-rich and GC-rich branches within a new subfamily to be named the Deltaherpesvirinae, which evolved separately from all other mammalian herpesviruses about100 million years ago.
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Keita MB, Hamad I, Bittar F. Looking in apes as a source of human pathogens. Microb Pathog 2014; 77:149-54. [PMID: 25220240 DOI: 10.1016/j.micpath.2014.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/05/2014] [Indexed: 12/27/2022]
Abstract
Because of the close genetic relatedness between apes and humans, apes are susceptible to many human infectious agents and can serve as carriers of these pathogens. Consequently, they present a serious health hazard to humans. Moreover, many emerging infectious diseases originate in wildlife and continue to threaten human populations, especially vector-borne diseases described in great apes, such as malaria and rickettsiosis. These wild primates may be permanent reservoirs and important sources of human pathogens. In this special issue, we report that apes, including chimpanzees (Pan troglodytes), bonobos (Pan paniscus), gorillas (Gorilla gorilla and Gorilla beringei), orangutans (Pongo pygmaeus and Pongo abelii), gibbons (Hylobates spp., Hoolock spp. and Nomascus spp) and siamangs (Symphalangus syndactylus syndactylus and Symphalangus continentis), have many bacterial, viral, fungal and parasitic species that are capable of infecting humans. Serious measures should be adopted in tropical forests and sub-tropical areas where habitat overlaps are frequent to survey and prevent infectious diseases from spreading from apes to people.
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Affiliation(s)
- Mamadou B Keita
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Ibrahim Hamad
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - Fadi Bittar
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France.
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African great apes are naturally infected with roseoloviruses closely related to human herpesvirus 7. J Virol 2014; 88:13212-20. [PMID: 25187544 DOI: 10.1128/jvi.01490-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Primates are naturally infected with herpesviruses. During the last 15 years, the search for homologues of human herpesviruses in nonhuman primates allowed the identification of numerous viruses belonging to the different herpesvirus subfamilies and genera. No simian homologue of human herpesvirus 7 (HHV7) has been reported to date. To investigate the putative existence of HHV7-like viruses in African great apes, we applied the consensus-degenerate hybrid oligonucleotide primers (CODEHOP) program-mediated PCR strategy to blood DNA samples from the four common chimpanzee subspecies (Pan troglodytes verus, P. t. ellioti, P. t. troglodytes, and P. t. schweinfurthii), pygmy chimpanzees (Pan paniscus), as well as lowland gorillas (Gorilla gorilla gorilla). This study led to the discovery of a novel roseolovirus close to HHV7 in each of these nonhuman primate species and subspecies. Generation of the partial glycoprotein B (1,111-bp) and full-length DNA polymerase (3,036/3,042-bp) gene sequences allowed the deciphering of their evolutionary relationships. Phylogenetic analyses revealed that HHV7 and its African great ape homologues formed well-supported monophyletic lineages whose topological resemblance to the host phylogeny is suggestive of virus-host codivergence. Notably, the evolutionary branching points that separate HHV7 from African great ape herpesvirus 7 are remarkably congruent with the dates of divergence of their hosts. Our study shows that African great apes are hosts of human herpesvirus homologues, including HHV7 homologues, and that the latter, like other DNA viruses that establish persistent infections, have cospeciated with their hosts. IMPORTANCE Human herpesviruses are known to possess simian homologues. However, surprisingly, none has been identified to date for human herpesvirus 7 (HHV7). This study is the first to describe simian homologues of HHV7. The extensive search performed on almost all African great ape species and subspecies, i.e., common chimpanzees of the four subspecies, bonobos, and lowland gorillas, has allowed characterization of a specific virus in each. Genetic characterization of the partial glycoprotein B and full-length DNA polymerase gene sequences, followed by their phylogenetic analysis and estimation of divergence times, has shed light on the evolutionary relationships of these viruses. In this respect, we conclusively demonstrate the cospeciation between these new viruses and their hosts and report cases of cross-species transmission between two common chimpanzee subspecies in both directions.
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Absence of frequent herpesvirus transmission in a nonhuman primate predator-prey system in the wild. J Virol 2013; 87:10651-9. [PMID: 23885068 DOI: 10.1128/jvi.01104-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Emergence of viruses into the human population by transmission from nonhuman primates (NHPs) represents a serious potential threat to human health that is primarily associated with the increased bushmeat trade. Transmission of RNA viruses across primate species appears to be relatively frequent. In contrast, DNA viruses appear to be largely host specific, suggesting low transmission potential. Herein, we use a primate predator-prey system to study the risk of herpesvirus transmission between different primate species in the wild. The system was comprised of western chimpanzees (Pan troglodytes verus) and their primary (western red colobus, Piliocolobus badius badius) and secondary (black-and-white colobus, Colobus polykomos) prey monkey species. NHP species were frequently observed to be coinfected with multiple beta- and gammaherpesviruses (including new cytomegalo- and rhadinoviruses). However, despite frequent exposure of chimpanzees to blood, organs, and bones of their herpesvirus-infected monkey prey, there was no evidence for cross-species herpesvirus transmission. These findings suggest that interspecies transmission of NHP beta- and gammaherpesviruses is, at most, a rare event in the wild.
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Calvignac-Spencer S, Leendertz SAJ, Gillespie TR, Leendertz FH. Wild great apes as sentinels and sources of infectious disease. Clin Microbiol Infect 2012; 18:521-7. [PMID: 22448813 DOI: 10.1111/j.1469-0691.2012.03816.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Emerging zoonotic infectious diseases pose a serious threat to global health. This is especially true in relation to the great apes, whose close phylogenetic relationship with humans results in a high potential for microorganism exchange. In this review, we show how studies of the microorganisms of wild great apes can lead to the discovery of novel pathogens of importance for humans. We also illustrate how these primates, living in their natural habitats, can serve as sentinels for outbreaks of human disease in regions with a high likelihood of disease emergence. Greater sampling efforts and improvements in sample preservation and diagnostic capacity are rapidly improving our understanding of the diversity and distribution of microorganisms in wild great apes. Linking non-invasive diagnostic data with observational health data from great apes habituated to human presence is a promising approach for the discovery of pathogens of high relevance for humans.
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Abstract
Cytomegalovirus (CMV) infection is the most common opportunistic infection in immunosuppressed individuals, such as transplant recipients or people living with HIV/AIDS, and congenital CMV is the leading viral cause of developmental disabilities in infants. Due to the highly species-specific nature of CMV, animal models that closely recapitulate human CMV (HCMV) are of growing importance for vaccine development. Here we present the genomic sequence of a novel nonhuman primate CMV from cynomolgus macaques (Macaca fascicularis; CyCMV). CyCMV (Ottawa strain) was isolated from the urine of a healthy, captive-bred, 4-year-old cynomolgus macaque of Philippine origin, and the viral genome was sequenced using next-generation Illumina sequencing to an average of 516-fold coverage. The CyCMV genome is 218,041 bp in length, with 49.5% G+C content and 84% protein-coding density. We have identified 262 putative open reading frames (ORFs) with an average coding length of 789 bp. The genomic organization of CyCMV is largely colinear with that of rhesus macaque CMV (RhCMV). Of the 262 CyCMV ORFs, 137 are homologous to HCMV genes, 243 are homologous to RhCMV 68.1, and 200 are homologous to RhCMV 180.92. CyCMV encodes four ORFs that are not present in RhCMV strain 68.1 or 180.92 but have homologies with HCMV (UL30, UL74A, UL126, and UL146). Similar to HCMV, CyCMV does not produce the RhCMV-specific viral homologue of cyclooxygenase-2. This newly characterized CMV may provide a novel model in which to study CMV biology and HCMV vaccine development.
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29
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Tsuda Y, Caposio P, Parkins CJ, Botto S, Messaoudi I, Cicin-Sain L, Feldmann H, Jarvis MA. A replicating cytomegalovirus-based vaccine encoding a single Ebola virus nucleoprotein CTL epitope confers protection against Ebola virus. PLoS Negl Trop Dis 2011; 5:e1275. [PMID: 21858240 PMCID: PMC3153429 DOI: 10.1371/journal.pntd.0001275] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/29/2011] [Indexed: 12/22/2022] Open
Abstract
Background Human outbreaks of Ebola virus (EBOV) are a serious human health concern in Central Africa. Great apes (gorillas/chimpanzees) are an important source of EBOV transmission to humans due to increased hunting of wildlife including the ‘bush-meat’ trade. Cytomegalovirus (CMV) is an highly immunogenic virus that has shown recent utility as a vaccine platform. CMV-based vaccines also have the unique potential to re-infect and disseminate through target populations regardless of prior CMV immunity, which may be ideal for achieving high vaccine coverage in inaccessible populations such as great apes. Methodology/Principal Findings We hypothesize that a vaccine strategy using CMV-based vectors expressing EBOV antigens may be ideally suited for use in inaccessible wildlife populations. To establish a ‘proof-of-concept’ for CMV-based vaccines against EBOV, we constructed a mouse CMV (MCMV) vector expressing a CD8+ T cell epitope from the nucleoprotein (NP) of Zaire ebolavirus (ZEBOV) (MCMV/ZEBOV-NPCTL). MCMV/ZEBOV-NPCTL induced high levels of long-lasting (>8 months) CD8+ T cells against ZEBOV NP in mice. Importantly, all vaccinated animals were protected against lethal ZEBOV challenge. Low levels of anti-ZEBOV antibodies were only sporadically detected in vaccinated animals prior to ZEBOV challenge suggesting a role, at least in part, for T cells in protection. Conclusions/Significance This study demonstrates the ability of a CMV-based vaccine approach to protect against an highly virulent human pathogen, and supports the potential for ‘disseminating’ CMV-based EBOV vaccines to prevent EBOV transmission in wildlife populations. Human outbreaks of hemorrhagic disease caused by Ebola virus (EBOV) are a serious health concern in Central Africa. Great apes (gorillas/chimpanzees) are an important source of EBOV transmission to humans. Candidate EBOV vaccines do not spread from the initial vaccinee. In addition to being highly immunogenic, vaccines based on the cytomegalovirus (CMV) platform have the unique potential to re-infect and disseminate through target populations. To explore the utility of CMV-based vaccines against EBOV, we constructed a mouse CMV (MCMV) vector expressing a region of nucleoprotein (NP) of Zaire ebolavirus (ZEBOV) (MCMV/ZEBOV-NPCTL). MCMV/ZEBOV-NPCTL induced high levels of long-lasting CD8+ T cells against ZEBOV NP in mice. Importantly, all vaccinated animals were protected against lethal ZEBOV challenge. The absence of ZEBOV neutralizing and only low, sporadic levels of total anti-ZEBOV IgG antibodies in protected animals prior to ZEBOV challenge indicate a role, albeit perhaps not exclusive, for CD8+ T cells in mediating protection. This study demonstrates the ability of a CMV-based vaccine approach to protect against ZEBOV, and provides a ‘proof-of-concept’ for the potential for a ‘disseminating’ CMV-based EBOV vaccine to prevent EBOV transmission in wild animal populations.
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Affiliation(s)
- Yoshimi Tsuda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Patrizia Caposio
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Christopher J. Parkins
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Sara Botto
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Ilhem Messaoudi
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Luka Cicin-Sain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Michael A. Jarvis
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Portland, Oregon, United States of America
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, United States of America
- * E-mail:
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Ehlers B, Mugisha L, Leendertz FH. LETTER TO THE EDITOR: Reply to the Comment by Gessain et al. on Mugisha et al. J Med Primatol 2010; 39: 71-76. J Med Primatol 2010. [DOI: 10.1111/j.1600-0684.2010.00418.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Deckers M, Hofmann J, Kreuzer KA, Reinhard H, Edubio A, Hengel H, Voigt S, Ehlers B. High genotypic diversity and a novel variant of human cytomegalovirus revealed by combined UL33/UL55 genotyping with broad-range PCR. Virol J 2009; 6:210. [PMID: 19941648 PMCID: PMC2789067 DOI: 10.1186/1743-422x-6-210] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 11/26/2009] [Indexed: 11/10/2022] Open
Abstract
The known strains of human cytomegalovirus (HCMV) represent genotypic variants of a single species, and HCMV genotypic variability has been studied in order to reveal correlations between different disease patterns and the presence of certain HCMV genotypes, either as single or as multiple infections. The methods used for the detection of HCMV genotypes have not always been sophisticated enough to achieve complete comprehensiveness, mainly because only one genotype is usually detected in a certain specimen, due to primer specificity and genome copy number. To improve detection of variant HCMV genotypes in mixed infections, we developed PCR assays with degenerate primers targeting two variable HCMV genes, glycoprotein B (gB, UL55) and the G-protein-coupled receptor gene UL33. Primers were designed to bind conserved sites in the genomes of HCMV variants and great ape CMVs. To analyse if samples contained one or more HCMV genotypic variants, PCR assays were supplemented with oligonucleotides containing locked nucleic acids. This broad-range PCR methodology and subsequent sequence analysis detected all gB/UL55 and UL33 genotypic variants known to date in primary clinical specimens, but also revealed that many samples contained genotype mixtures. Importantly, a novel UL33 genotypic variant could be discovered in several specimens, and one HCMV isolate was plaque-purified containing the novel UL33 genotype and a so far undescribed variant of gB.
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Affiliation(s)
- Merlin Deckers
- P14 Molekulare Genetik und Epidemiologie von Herpesviren, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany.
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Ehlers B, Spiess K, Leendertz F, Peeters M, Boesch C, Gatherer D, McGeoch DJ. Lymphocryptovirus phylogeny and the origins of Epstein-Barr virus. J Gen Virol 2009; 91:630-42. [PMID: 19923263 DOI: 10.1099/vir.0.017251-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Specimens from wild and captive primates were collected and novel members of the genus Lymphocryptovirus (subfamily Gammaherpesvirinae) were searched for utilizing PCR for the DNA polymerase gene. Twenty-one novel viruses were detected. Together with previous findings, more than 50 distinct lymphocryptoviruses (LCVs) are now known, with hosts from six primate families (Hominidae, Hylobatidae, Cercopithecidae, Atelidae, Cebidae and Pitheciidae). Further work extended genomic sequences for 25 LCVs to 3.4-7.4 kbp. Phylogenetic trees were constructed, based on alignments of protein sequences inferred from the LCV genomic data. The LCVs fell into three major clades: Clade A, comprising New World viruses; Clade B, containing both Old World monkey viruses and hominoid viruses including Epstein-Barr virus (EBV); and Clade C, containing other hominoid viruses. By comparison with the primate tree, it was proposed that major elements of the LCV tree represented synchronous evolution with host lineages, with the earliest node in both trees being the separation of Old and New World lines, but that some virus lineages originated by interspecies transfer. From comparisons of branch lengths, it was inferred that evolutionary substitution in Clade B has proceeded more slowly than elsewhere in the LCV tree. It was estimated that in Clade B a subclade containing EBV, a gorilla virus and two chimpanzee viruses derived from an Old World monkey LCV line approximately 12 million years ago, and another subclade containing an orang-utan virus and a gibbon virus derived from a macaque LCV line approximately 1.2 million years ago.
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Affiliation(s)
- Bernhard Ehlers
- Research Group Molecular Genetics and Epidemiology of Herpesviruses, Robert Koch-Institut, D-13353 Berlin, Germany.
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Mugisha L, Leendertz FH, Opuda-Asibo J, Olobo JO, Ehlers B. A novel herpesvirus in the sanctuary chimpanzees on Ngamba Island in Uganda. J Med Primatol 2009; 39:71-6. [PMID: 19900168 DOI: 10.1111/j.1600-0684.2009.00396.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Recent studies in non-human primates have led to the discovery of novel primate herpesviruses. In order to get more information on herpesvirus infections in apes, we studied wild born captive chimpanzees. METHODS Chimpanzees of the Ngamba island sanctuary, Uganda, were analyzed with pan-herpes polymerase chain reaction (PCR) targeting the herpesvirus DNA polymerase gene and the glycoprotein B gene. The obtained sequences were connected by long-distance PCR, and analyzed phylogenetically. RESULTS Twenty-one of 40 individuals were infected with members of the Gammaherpesvirinae, two of them with a novel member of this subfamily. Phylogenetically, the novel virus fell into a clade of primate rhadinoviruses and the Kaposi sarcoma herpesvirus (human herpesvirus 8), representing a third distinct rhadinovirus in chimpanzees. CONCLUSION Non-human primates harbor several herpesviruses many of which are still unknown. This has implications to management of primates in sanctuaries requiring continuous updates on the management protocols to deal with potential occupational pathogens.
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Affiliation(s)
- L Mugisha
- Chimpanzee Sanctuary & Wildlife Conservation Trust (CSWCT), Entebbe, Uganda
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Lacoste V, Lavergne A, de Thoisy B, Pouliquen JF, Gessain A. Genetic diversity and molecular evolution of human and non-human primate Gammaherpesvirinae. INFECTION GENETICS AND EVOLUTION 2009; 10:1-13. [PMID: 19879975 DOI: 10.1016/j.meegid.2009.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 10/19/2009] [Accepted: 10/21/2009] [Indexed: 12/26/2022]
Abstract
The Gammaherpesvirinae sub-family is divided into two genera: Lymphocryptovirus and Rhadinovirus. Until the middle of the 1990s, the Rhadinovirus genus was only represented by Herpesvirus saimiri and Herpesvirus ateles, which infect New World monkey species. Until the year 2000, Epstein-Barr virus (EBV), the human prototype of the Lymphocryptovirus, and simian homologues had only been detected in humans and Old World non-human primates. It was thought, therefore, that the separation of the continents had resulted in drastic changes in Gammaherpesvirinae evolution. The discovery of Kaposi's sarcoma-associated herpesvirus in humans, belonging to the Rhadinovirus, followed by the identification of CalHV3 (Callitrichine herpesvirus 3), a lymphocryptovirus of the marmoset, challenged this paradigm. The description of numerous viruses belonging to this sub-family from various Old and New World primate species enabled a cospeciation hypothesis for these viruses and their hosts to be developed. This review focuses on the current knowledge of primate Gammaherpesvirinae genetic diversity and molecular evolution. We discuss the various theories based on current genetic data regarding evolutionary relationships between lymphocryptoviruses of Old World primates, the use of these data as a tool to study evolutionary relationships between New World monkey species, and the possible existence of a ninth human herpesvirus belonging to the Rhadinovirus genus.
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Affiliation(s)
- Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de Guyane, 23 avenue Pasteur, BP6010, 97306 Cayenne Cedex, French Guiana.
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