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Locarnini SA, Littlejohn M, Yuen LKW. Origins and Evolution of the Primate Hepatitis B Virus. Front Microbiol 2021; 12:653684. [PMID: 34108947 PMCID: PMC8180572 DOI: 10.3389/fmicb.2021.653684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
Recent interest in the origins and subsequent evolution of the hepatitis B virus (HBV) has strengthened with the discovery of ancient HBV sequences in fossilized remains of humans dating back to the Neolithic period around 7,000 years ago. Metagenomic analysis identified a number of African non-human primate HBV sequences in the oldest samples collected, indicating that human HBV may have at some stage, evolved in Africa following zoonotic transmissions from higher primates. Ancestral genotype A and D isolates were also discovered from the Bronze Age, not in Africa but rather Eurasia, implying a more complex evolutionary and migratory history for HBV than previously recognized. Most full-length ancient HBV sequences exhibited features of inter genotypic recombination, confirming the importance of recombination and the mutation rate of the error-prone viral replicase as drivers for successful HBV evolution. A model for the origin and evolution of HBV is proposed, which includes multiple cross-species transmissions and favors subsequent recombination events that result in a pathogen and can successfully transmit and cause persistent infection in the primate host.
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Affiliation(s)
- Stephen A Locarnini
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Lilly K W Yuen
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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2
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Cagliani R, Mozzi A, Pontremoli C, Sironi M. Evolution and Origin of Human Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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3
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Glebe D, Goldmann N, Lauber C, Seitz S. HBV evolution and genetic variability: Impact on prevention, treatment and development of antivirals. Antiviral Res 2020; 186:104973. [PMID: 33166575 DOI: 10.1016/j.antiviral.2020.104973] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Hepatitis B virus (HBV) poses a major global health burden with 260 million people being chronically infected and 890,000 dying annually from complications in the course of the infection. HBV is a small enveloped virus with a reverse-transcribed DNA genome that infects hepatocytes and can cause acute and chronic infections of the liver. HBV is endemic in humans and apes representing the prototype member of the viral family Hepadnaviridae and can be divided into 10 genotypes. Hepadnaviruses have been found in all vertebrate classes and constitute an ancient viral family that descended from non-enveloped progenitors more than 360 million years ago. The de novo emergence of the envelope protein gene was accompanied with the liver-tropism and resulted in a tight virus-host association. The oldest HBV genomes so far have been isolated from human remains of the Bronze Age and the Neolithic (~7000 years before present). Despite the remarkable stability of the hepadnaviral genome over geological eras, HBV is able to rapidly evolve within an infected individual under pressure of the immune response or during antiviral treatment. Treatment with currently available antivirals blocking intracellular replication of HBV allows controlling of high viremia and improving liver health during long-term therapy of patients with chronic hepatitis B (CHB), but they are not sufficient to cure the disease. New therapy options that cover all HBV genotypes and emerging viral variants will have to be developed soon. In addition to the antiviral treatment of chronically infected patients, continued efforts to expand the global coverage of the currently available HBV vaccine will be one of the key factors for controlling the rising global spread of HBV. Certain improvements of the vaccine (e.g. inclusion of PreS domains) could counteract known problems such as low or no responsiveness of certain risk groups and waning anti-HBs titers leading to occult infections, especially with HBV genotypes E or F. But even with an optimal vaccine and a cure for hepatitis B, global eradication of HBV would be difficult to achieve because of an existing viral reservoir in primates and bats carrying closely related hepadnaviruses with zoonotic potential.
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Affiliation(s)
- Dieter Glebe
- Institute of Medical Virology, Justus Liebig University of Giessen, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Schubertstr. 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany.
| | - Nora Goldmann
- Institute of Medical Virology, Justus Liebig University of Giessen, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Schubertstr. 81, 35392, Giessen, Germany
| | - Chris Lauber
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany; Research Group Computational Virology, Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz Centre for Infection Research and the Hannover Medical School, Cluster of Excellence RESIST, Hannover Medical School, 30625, Hannover, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany; Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120, Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany.
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4
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Datta S. Excavating new facts from ancient Hepatitis B virus sequences. Virology 2020; 549:89-99. [PMID: 32858309 DOI: 10.1016/j.virol.2020.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/02/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022]
Abstract
Recently, two independent studies discovered 15 ancient Hepatitis B virus (aHBV) sequences, of which 7 dated back to the Neolithic age (NA) and the Bronze Age (BA). In the present research, all the available aHBV sequences were collectively re-analysed with reference to extant HBV diversity to understand the role of these aHBV genotypes in evolution of extant HBV genetic diversity. Several intergenotype recombination events were documented, which corroborated well with population admixture and ancient human migration. Present analyses suggested replacement of HBV genotype associated with early Neolithic European farming cultures by the migrating steppe people, during Bronze Age Steppe migration. Additionally, detailed analyses of recombinations revealed evolution of a number of extant genotypes and suggested their possible site of origin. Through this manuscript, novel and important findings of the analyses are communicated.
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Affiliation(s)
- Sibnarayan Datta
- Molecular Virology Laboratory, Entomology & Biothreat Management Division, Defence Research Laboratory, Defence R&D Organization (DRDO), PO Bag 02, Tezpur HPO, Assam, 784001, India.
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Trumble BC, Finch CE. THE EXPOSOME IN HUMAN EVOLUTION: FROM DUST TO DIESEL. THE QUARTERLY REVIEW OF BIOLOGY 2019; 94:333-394. [PMID: 32269391 PMCID: PMC7141577 DOI: 10.1086/706768] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Global exposures to air pollution and cigarette smoke are novel in human evolutionary history and are associated with about 16 million premature deaths per year. We investigate the history of the human exposome for relationships between novel environmental toxins and genetic changes during human evolution in six phases. Phase I: With increased walking on savannas, early human ancestors inhaled crustal dust, fecal aerosols, and spores; carrion scavenging introduced new infectious pathogens. Phase II: Domestic fire exposed early Homo to novel toxins from smoke and cooking. Phases III and IV: Neolithic to preindustrial Homo sapiens incurred infectious pathogens from domestic animals and dense communities with limited sanitation. Phase V: Industrialization introduced novel toxins from fossil fuels, industrial chemicals, and tobacco at the same time infectious pathogens were diminishing. Thereby, pathogen-driven causes of mortality were replaced by chronic diseases driven by sterile inflammogens, exogenous and endogenous. Phase VI: Considers future health during global warming with increased air pollution and infections. We hypothesize that adaptation to some ancient toxins persists in genetic variations associated with inflammation and longevity.
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Affiliation(s)
- Benjamin C Trumble
- School of Human Evolution & Social Change and Center for Evolution and Medicine, Arizona State University Tempe, Arizona 85287 USA
| | - Caleb E Finch
- Leonard Davis School of Gerontology and Dornsife College, University of Southern California Los Angeles, California 90089-0191 USA
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Li Y, Wei T, Yan L, Yang Z, Huang Q, Shi Y, Wang L. Association of interleukin-28B polymorphisms with platelet count and liver function recovery after liver transplant. Medicine (Baltimore) 2017; 96:e8219. [PMID: 29095252 PMCID: PMC5682771 DOI: 10.1097/md.0000000000008219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 09/10/2017] [Accepted: 09/13/2017] [Indexed: 02/05/2023] Open
Abstract
The present genome-wide association study investigated the relationship of interleukin 28B (IL-28B) genetic variants with HBV susceptibility and prognosis of HBV-infected patients. This study aims to examine the role of IL-28B polymorphisms on transplant etiologies and the liver function recovery in Chinese liver transplant recipients.A total of 231 liver transplant recipients were enrolled in the study. The transplant etiologies included progressive HBV hepatitis, HBV-related liver cirrhosis (LC), HBV-related hepatocellular carcinoma (HCC), and non-HBV-related disease. All recipients were in stable condition before transplantation. Three single nucleotide polymorphisms (SNPs) of IL-28B (rs12979860, rs12980275, rs8099917) of recipients were analyzed by high-resolution melting (HRM) curve analysis. Liver function, blood cell count, and coagulation function were regularly tested before and for next 5 years after transplantation.No significant association was found between IL-28B gene polymorphisms and transplant etiologies. Peripheral platelet count in the third and fourth days after transplantation were significantly higher in recipients carrying IL-28B rs12979860 T allele, or rs8099917 C allele (P < .016666667), while there were no significant differences between these variants and International Normalized Ratio (INR) levels. In addition, gamma-glutamyltransferase (GGT) levels in recipients with rs12980275 G allele were higher than those in the wide-type recipients before transplantation (P < .016666667, respectively); nevertheless, no influence of these variants on GGT recovery was observed after transplantation.Genetic variations of IL-28B might impact on liver function recovery by influencing peripheral platelet counts and reducing liver inflammation, but have weak association with transplant etiologies.
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Affiliation(s)
- Yi Li
- Department of Laboratory Medicine
| | - Tiantian Wei
- Kidney Research Institute, Division of Nephrology, West China Hospital
| | - Lin Yan
- Department of Laboratory Medicine
| | - Zhiqiang Yang
- West China Medical School, Sichuan University, Chengdu, China
| | - Qian Huang
- West China Medical School, Sichuan University, Chengdu, China
| | - Yunying Shi
- Kidney Research Institute, Division of Nephrology, West China Hospital
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Rasche A, Souza BFDCD, Drexler JF. Bat hepadnaviruses and the origins of primate hepatitis B viruses. Curr Opin Virol 2016; 16:86-94. [PMID: 26897577 DOI: 10.1016/j.coviro.2016.01.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 02/07/2023]
Abstract
The origin of primate HBV (family Hepadnaviridae) is unknown. Hepadnaviruses are ancient pathogens and may have been associated with old mammalian lineages like bats for prolonged time. Indeed, the genetic diversity of bat hepadnaviruses exceeds that of extant hepadnaviruses in other host orders, suggesting a long evolution of hepadnaviruses in bats. Strikingly, a recently detected New World bat hepadnavirus is antigenically related to HBV and can infect human hepatocytes. Together with genetically diverse hepadnaviruses from New World rodents and a non-human primate, these viruses argue for a New World origin of ancestral orthohepadnaviruses. Multiple host switches of bat and primate viruses are evident and bats are likely sources of ancestral hepadnaviruses acquired by primates.
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Affiliation(s)
- Andrea Rasche
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Breno Frederico de Carvalho Dominguez Souza
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany; Infectious Diseases Research Laboratory, University Hospital Professor Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany; German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Germany.
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Littlejohn M, Locarnini S, Yuen L. Origins and Evolution of Hepatitis B Virus and Hepatitis D Virus. Cold Spring Harb Perspect Med 2016; 6:a021360. [PMID: 26729756 DOI: 10.1101/cshperspect.a021360] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Members of the family Hepadnaviridae fall into two subgroups: mammalian and avian. The detection of endogenous avian hepadnavirus DNA integrated into the genomes of zebra finches has revealed a deep evolutionary origin of hepadnaviruses that was not previously recognized, dating back at least 40 million and possibly >80 million years ago. The nonprimate mammalian members of the Hepadnaviridae include the woodchuck hepatitis virus (WHV), the ground squirrel hepatitis virus, and arctic squirrel hepatitis virus, as well as a number of members of the recently described bat hepatitis virus. The identification of hepatitis B viruses (HBVs) in higher primates, such as chimpanzee, gorilla, orangutan, and gibbons that cluster with the human HBV, as well as a number of recombinant forms between humans and primates, further implies a more complex origin of this virus. We discuss the current theories of the origin and evolution of HBV and propose a model that includes cross-species transmissions and subsequent recombination events on a genetic backbone of genotype C HBV infection. The hepatitis delta virus (HDV) is a defective RNA virus requiring the presence of the HBV for the completion of its life cycle. The origins of this virus remain unknown, although some recent studies have suggested an ancient African radiation. The age of the association between HDV and HBV is also unknown.
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Affiliation(s)
- Margaret Littlejohn
- Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne 3000, Australia
| | - Stephen Locarnini
- Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne 3000, Australia
| | - Lilly Yuen
- Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne 3000, Australia
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9
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Araujo NM. Hepatitis B virus intergenotypic recombinants worldwide: An overview. INFECTION GENETICS AND EVOLUTION 2015; 36:500-510. [PMID: 26299884 DOI: 10.1016/j.meegid.2015.08.024] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/11/2015] [Accepted: 08/19/2015] [Indexed: 02/07/2023]
Abstract
Novel variants generated by recombination events between different hepatitis B virus (HBV) genotypes have been increasingly documented worldwide, and the role of recombination in the evolutionary history of HBV is of significant research interest. In the present study, large-scale data retrieval and analysis on HBV intergenotypic recombinant genomes were performed. The geographical distribution of HBV recombinants as well as the molecular processes involved in recombination were examined. After review of published data, a total of 436 complete HBV sequences, previously identified as recombinants, were included in the recombination detection analysis. About 60% of HBV recombinants were B/C (n=179) and C/D (n=83) hybrids. A/B/C, A/C, A/C/G, A/D, A/E, A/G, B/C/U (U=unknown genotype), C/F, C/G, C/J, D/E, D/F, and F/G hybrids were additionally identified. HBV intergenotypic sequences were reported in almost all geographical regions with similar circulation patterns as their original genotypes, indicating the potential for spreading in a wide range of human populations and developing their own epidemiology. Recombination breakpoints were non-randomly distributed in the genome, and specific favored sites detected, such as within nt 1700-2000 and 2100-2300 regions, which displayed a statistically significant difference in comparison with the remaining genome. Elucidation of the effects of recombination events on the evolutionary history of HBV is critical to understand current and future evolution trends.
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Affiliation(s)
- Natalia M Araujo
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, 21040-360 Rio de Janeiro, RJ, Brazil.
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10
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Locarnini S, Littlejohn M, Aziz MN, Yuen L. Possible origins and evolution of the hepatitis B virus (HBV). Semin Cancer Biol 2013; 23:561-75. [PMID: 24013024 DOI: 10.1016/j.semcancer.2013.08.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/27/2013] [Indexed: 02/06/2023]
Abstract
All members of the family Hepadnaviridae are primarily viruses which contain double-stranded DNA genomes that are replicated via reverse transcription of a pregenomic RNA template. There are two subgroups within this family: mammalian and avian. The avian member's include the duck hepatitis B virus (DHBV), heron hepatitis B virus, Ross goose hepatitis B virus, stork hepatitis B virus and the recently identified parrot hepatitis B virus. More recently, the detection of endogenous avian hepadnavirus DNA integrated into the genomes of zebra finches has revealed a deep evolutionary origin of hepadnaviruses that was not previously recognised, dating back over 40 million years ago. The non-primate mammalian members of the Hepadnaviridae include the woodchuck hepatitis virus (WHV), the ground squirrel hepatitis virus and arctic squirrel virus, as well as the recently described bat hepatitis virus. The identification of hepatitis B virus (HBV) in higher primates such as chimpanzee, gorilla, orangutan, and gibbons that cluster with the human genotypes further implies a more complex origin of this virus. By studying the molecular epidemiology of HBV in indigenous and relict populations in Asia-Pacific we propose a model for the origin and evolution of HBV that involves multiple cross-species transmissions and subsequent recombination events on a background of genotype C HBV infection.
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Affiliation(s)
- Stephen Locarnini
- Research & Molecular Development, Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia.
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11
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Liu B, Wen X, Huang C, Wei Y. Unraveling the complexity of hepatitis B virus: from molecular understanding to therapeutic strategy in 50 years. Int J Biochem Cell Biol 2013; 45:1987-96. [PMID: 23819994 DOI: 10.1016/j.biocel.2013.06.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 06/18/2013] [Accepted: 06/21/2013] [Indexed: 02/05/2023]
Abstract
Hepatitis B virus (HBV) is a well-known hepadnavirus with a double-stranded circular DNA genome. Although HBV was first described approximately 50 years ago, the precise mechanisms of HBV infection and effective therapeutic strategies remain unclear. Here, we focus on summarizing the complicated mechanisms of HBV replication and infection, as well as genomic factors and epigenetic regulation. Additionally, we discuss in vivo models of HBV, as well as diagnosis, prevention and therapeutic drugs for HBV. Together, the data in this 50-year review may provide new clues to elucidate molecular mechanisms of HBV pathogenesis and shed new light on the future HBV therapies.
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Affiliation(s)
- Bo Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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12
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Araujo NM, Araujo OC, Silva EM, Villela-Nogueira CA, Nabuco LC, Parana R, Bessone F, Gomes SA, Trepo C, Kay A. Identification of novel recombinants of hepatitis B virus genotypes F and G in human immunodeficiency virus-positive patients from Argentina and Brazil. J Gen Virol 2012; 94:150-158. [PMID: 23079380 DOI: 10.1099/vir.0.047324-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) genotype G (HBV/G) infection is almost always detected along with a co-infecting HBV strain that can supply HBeAg, typically HBV/A2. In this study we describe, in two human immunodeficiency virus (HIV)-positive patients from Argentina and Brazil, the first report of HBV/G infection in Argentina and co-circulation of HBV/G, HBV/F and G/F recombinants in the American continent. HBV isolates carrying the 36 bp insertion of HBV/G were the most prevalent in both patients, with >99 % of colonies hybridizing to a probe specific for this insertion. Phylogenetic analyses of full-length genomes and precore/core fragments revealed that F4 and F1b were the co-infecting subgenotypes in the Brazilian and Argentinian patients, respectively. Bootscanning analysis provided evidence of recombination in several clones from both patients, with recombination breakpoints located mainly at the precore/core region. These data should encourage further investigations on the clinical implications of HBV/G recombinants in HBV/HIV co-infected patients.
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Affiliation(s)
- Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Oscar C Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Edinete M Silva
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
| | - Cristiane A Villela-Nogueira
- Hepatology Division, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-970, Brazil
| | - Letícia C Nabuco
- Hepatology Division, Clementino Fraga Filho University Hospital, Federal University of Rio de Janeiro, Rio de Janeiro 21941-970, Brazil
| | - Raymundo Parana
- Department of Hepato-Gastroenterology, Prof. Edgard Santos University Hospital, Federal University of Bahia, Salvador 40110-060, Brazil
| | - Fernando Bessone
- Department of Gastroenterology and Hepatology, University of Rosario School of Medicine, Rosario 2000, Argentina
| | - Selma A Gomes
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Christian Trepo
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
| | - Alan Kay
- Centre de Recherche en Cancérologie de Lyon - INSERM U 1052/CNRS UMR 5286, 69424 Lyon Cedex 03, France
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Chen J, Li Y, Wang L, Fu Y, Liao Y, Zhang J. Association of three SNPs in interleukin-28B with graft hepatic dysfunction after liver transplantation in Chinese Han population. Gene 2012; 508:121-4. [PMID: 22967712 DOI: 10.1016/j.gene.2012.07.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 07/30/2012] [Indexed: 02/05/2023]
Abstract
BACKGROUND Recurrent graft infection limited the effect of LT, early recognition and prophylaxis of HBV recurrence are very important, and interleukin 28B (IL‐28B) gene was reported to be associated with HBV infection. AIMS To explore the association between IL-28B single-nucleotide polymorphisms (SNPs) and graft re-infection after liver transplantation(LT). METHODS 21 recipients with hepatitis B virus(HBV) recurrence and 157 recipients without HBV recurrence were included. We studied three SNPs in the promoter region of IL-28B gene at the positions rs12979860,rs12980275 and rs8099917 by HRM analysis (high-resolution melting curve analysis). RESULTS Hepatic allograft dysfunction was more likely to be associated with IL-28B SNPs. However, there was no significant difference in the frequencies of IL-28B gene distribution in recipients with or without HBV recurrence. CONCLUSION IL-28B gene polymorphism may be associated with the prognosis of LT recipients but it needs more experiments.
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Affiliation(s)
- Jie Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China
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Species association of hepatitis B virus (HBV) in non-human apes; evidence for recombination between gorilla and chimpanzee variants. PLoS One 2012; 7:e33430. [PMID: 22432021 PMCID: PMC3303819 DOI: 10.1371/journal.pone.0033430] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/08/2012] [Indexed: 01/28/2023] Open
Abstract
Hepatitis B virus (HBV) infections are widely distributed in humans, infecting approximately one third of the world's population. HBV variants have also been detected and genetically characterised from Old World apes; Gorilla gorilla (gorilla), Pan troglodytes (chimpanzee), Pongo pygmaeus (orang-utan), Nomascus nastusus and Hylobates pileatus (gibbons) and from the New World monkey, Lagothrix lagotricha (woolly monkey). To investigate species-specificity and potential for cross species transmission of HBV between sympatric species of apes (such as gorillas and chimpanzees in Central Africa) or between humans and chimpanzees or gorillas, variants of HBV infecting captive wild-born non-human primates were genetically characterised. 9 of 62 chimpanzees (11.3%) and two from 11 gorillas (18%) were HBV-infected (15% combined frequency), while other Old world monkey species were negative. Complete genome sequences were obtained from six of the infected chimpanzee and both gorillas; those from P. t .ellioti grouped with previously characterised variants from this subspecies. However, variants recovered from P. t. troglodytes HBV variants also grouped within this clade, indicative of transmission between sub-species, forming a paraphyletic clade. The two gorilla viruses were phylogenetically distinct from chimpanzee and human variants although one showed evidence for a recombination event with a P.t.e.-derived HBV variant in the partial X and core gene region. Both of these observations provide evidence for circulation of HBV between different species and sub-species of non-human primates, a conclusion that differs from the hypothesis if of strict host specificity of HBV genotypes.
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15
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Mulyanto, Pancawardani P, Depamede SN, Wahyono A, Jirintai S, Nagashima S, Takahashi M, Nishizawa T, Okamoto H. Identification of four novel subgenotypes (C13-C16) and two inter-genotypic recombinants (C12/G and C13/B3) of hepatitis B virus in Papua province, Indonesia. Virus Res 2011; 163:129-40. [PMID: 21925554 DOI: 10.1016/j.virusres.2011.09.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 09/02/2011] [Accepted: 09/02/2011] [Indexed: 02/07/2023]
Abstract
Four novel subgenotypes (C6, C11, C12, and D6) of hepatitis B virus (HBV) were identified in Papua, a multiethnic province of Indonesia. To characterize the HBV strains in Papua, serum samples collected from 515 indigenous inhabitants (mean age: 26.6±9.6 years) in a previously unexamined area, Nabire, located in northern Papua, were used in the present study. Among 46 samples whose 1.6-kilobase (kb) HBV DNA sequence was amplified, 38 (83%) were typeable into known subgenotypes [B3 (n=4), C1 (n=2), C5, (n=1), C6 (n=5), C12 (n=13), and D6 (n=13)]. An analysis of the full-length sequence of the eight remaining HBV/C isolates whose sequence was either unclassifiable or uncertain within the 1.6-kb sequence showed no significant evidence of recombination in six isolates, and inter-genotypic recombination in two isolates (NAB20 and NAB46). By pairwise comparisons and a maximum-likelihood phylogenetic analysis, six non-recombinant isolates were considered significantly remote from known HBV/C isolates of subgenotypes C1-C12, and were classifiable into four novel subgenotypes (tentatively designated C13-C16). NAB20 and NAB46 were hybrids of C13/B3 and C12/G, respectively, displaying recombination breakpoints in the 5'-terminus of the P gene. Notably, the distribution of presumably indigenous subgenotypes C11-C16 was associated with particular language speakers in Papua.
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Affiliation(s)
- Mulyanto
- Immunobiology Laboratory, Faculty of Medicine, University of Mataram, Mataram, Indonesia
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16
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Chen XL, Sun DX, Zhang XL. Hepatitis B virus genotypes. Shijie Huaren Xiaohua Zazhi 2011; 19:389-393. [DOI: 10.11569/wcjd.v19.i4.389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is a member of the hepadnavirus family and can lead to severe liver disease. HBV has a very high genetic variability. Currently, eight genotypes of HBV have been recognized, and most genotypes are now divided into subgenotypes with distinct virological and epidemiological properties. In addition, recombination among HBV genotypes increases the variability of HBV. This review summarizes current knowledge of the epidemiology of genetic variability in hepadnaviruses and, due to rapid progress in the field, updates several recent reviews on HBV genotypes and subgenotypes.
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Mugisha L, Kaiser M, Ellerbrok H, Pauli G, Opuda-Asibo J, Joseph OO, Leendertz FH. The "original" hepatitis B virus of Eastern chimpanzees (Pan trogrodytes schweinfurthii). Virus Res 2010; 155:372-5. [PMID: 20970465 DOI: 10.1016/j.virusres.2010.10.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/30/2010] [Accepted: 10/14/2010] [Indexed: 12/19/2022]
Abstract
Little is known about Hepatitis B Virus (HBV) infections in chimpanzees. Therefore, we investigated the prevalence of chimpanzee HBV (chHBV) infections in captive, wild born chimpanzees in the sanctuary on Ngamba Island, Uganda and one sample from a wild free ranging chimpanzee. In one third of the plasma samples (32.4%; 12/37) we detected antibodies to Hepatitis B (core) antigen. Amongst those individuals HBV DNA was detected in one captive wild born and the wild chimpanzee. In contrast to the only available earlier described HBV sequence from the subspecies Pan troglodytes schweinfurthii, there was no evidence of recombination with human HBV. Our sequences therefore are likely to present the "original" chHBV from P. t. schweinfurthii.
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Affiliation(s)
- Lawrence Mugisha
- Chimpanzee Sanctuary & Wildlife Conservation Trust, PO Box 884, Entebbe, Uganda
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Fang ZL, Hué S, Sabin CA, Li GJ, Yang JY, Chen QY, Fang KX, Huang J, Wang XY, Harrison TJ. A complex hepatitis B virus (X/C) recombinant is common in Long An county, Guangxi and may have originated in southern China. J Gen Virol 2010; 92:402-11. [PMID: 20965984 PMCID: PMC3081081 DOI: 10.1099/vir.0.026666-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recently, a complex (X/C) hepatitis B virus (HBV) recombinant, first reported in 2000, was proposed as a new genotype; although this was refuted immediately because the strains differ by less than 8 % in nucleotide distance from genotype C. Over 13.5 % (38/281) of HBV isolates from the Long An cohort in China were not assigned to a specific genotype, using current genotyping tools to analyse surface ORF sequences, and these have about 98 % similarity to the X/C recombinants. To determine whether this close identity extends to the full-length sequences and to investigate the evolutionary history of the Long An X/C recombinants, 17 complete genome sequences were determined. They are highly similar (96–99 %) to the Vietnamese strains and, although some reach or exceed 8 % nucleotide sequence difference from all known genotypes, they cluster together in the same clade, separating in a phylogenetic tree from the genotype C branch. Analysis of recombination reveals that all but one of the Long An isolates resembles the Vietnamese isolates in that they result from apparent recombination between genotype C and a parent of unknown genotype (X), which shows similarity in part to genotype G. The exception, isolate QL523, has a greater proportion of genotype C parent. Phylogeographic analysis reveals that these recombinants probably arose in southern China and spread later to Vietnam and Laos.
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19
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Detecting putative recombination events of hepatitis B virus: An updated comparative genome analysis. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11434-010-3109-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Li W, She R, Liu L, You H, Yin J. Prevalence of a virus similar to human hepatitis B virus in swine. Virol J 2010; 7:60. [PMID: 20233455 PMCID: PMC2850902 DOI: 10.1186/1743-422x-7-60] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 03/17/2010] [Indexed: 12/17/2022] Open
Abstract
Background The objective of this study is to established evidence of the existence of a novel member of the hepadnavirus family endemic in swine. Temporarily this virus was designated as swine hepatitis B virus (SHBV). This SHBV can be detected by using human hepatitis B virus diagnostic kits including ELISA, immunohistochemical staining, and transmission electron microscopy (TEM). Also seroprevalence of pig farms in Beijing, China, and pathological features of SHBV infection was determined. Results Screened result shows that overall prevalence of HBsAg was 24.8%, closed to that of anti-HBsAg, whereas HBeAg and anti-HBe were barely detectable. The distribution of HBsAg and HBcAg was examined by immunohistochemistry of liver samples. Typical hepatitis pathological change, such as spotty parenchymal cell degeneration, necrosis of hepatocytes and proliferation of fibrous connective tissue were observed during histopathological analysis. Analysis of HBsAg-positive serum with TEM revealed two morphologic forms, 20 nm and 40 nm sized particles, similar to small spherical and Danes particles of HBV. Observation of the ultrastructure of the liver also found HBV-like particles in the nucleus of hepatocytes. Conclusion Our research result implies that SHBV could be a causative agent of swine. The discovery of SHBV will unveil novel evolutionary aspects of hepatitis and provides new information for further hepadnavirus research.
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Affiliation(s)
- Wengui Li
- College of Veterinary Medicine, China Agricultural University, Beijing, China
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21
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Prevalence and phylogenetic analysis of hepatitis B virus among nonhuman primates in Taiwan. J Zoo Wildl Med 2009; 40:519-28. [PMID: 19746868 DOI: 10.1638/2008-0150.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hepatitis B virus (HBV) is a public health problem worldwide, and apart from infecting humans, HBV has been found in nonhuman primates. This study investigated the prevalence and phylogenetic analysis of hepatitis B virus (HBV) and hepatitis D virus (HDV) among nonhuman primates in Taiwan, an area where human HBV remains endemic. Serum samples from 286 captive nonhuman primates (i.e., 32 great apes [Pan troglodytes and Pongo pygmaeus], 42 gibbons [Hylobates sp. and Nomascus sp.], and 212 Cercopithecidae monkeys) were collected and tested for the presence of HBV- and HDV-specific serologic markers. None of the Cercopithecidae monkeys were reactive against serologic markers of HBV. In contrast, 21.9% (7/32) of great apes and 40.5% (17/42) of gibbons tested positive for at least one serologic marker of HBV. Of these, five gibbons were chronic HBV carriers, characterized by presence of HBV DNA and hepatitis B surface antigen in the serum. HBV DNA was also detected in the saliva of three of the chronic carries. None of these HBV carrier gibbons exhibited symptoms or significant change in serum clinical chemistry related to HBV infection. Phylogenetic analysis of the complete HBV genome revealed that gibbon viruses clustered with other HBV isolates of great apes and gibbons from Southeast Asia and separately from human-specific HBV. None of the HBV-infected animals were reactive against HDV. These findings indicate that HBV found in these animals is indigenous to their respective hosts and might have been introduced into Taiwan via the direct import of infected animals from Southeast Asia. To reduce the horizontal and vertical transmission of HBV in captive animals, the HBV carriers should be kept apart from uninfected animals.
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A genetic variant of hepatitis B virus divergent from known human and ape genotypes isolated from a Japanese patient and provisionally assigned to new genotype J. J Virol 2009; 83:10538-47. [PMID: 19640977 DOI: 10.1128/jvi.00462-09] [Citation(s) in RCA: 317] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) of a novel genotype (J) was recovered from an 88-year-old Japanese patient with hepatocellular carcinoma who had a history of residing in Borneo during the World War II. It was divergent from eight human (A to H) and four ape (chimpanzee, gorilla, gibbon, and orangutan) HBV genotypes, as well as from a recently proposed ninth human genotype I, by 9.9 to 16.5% of the entire genomic sequence and did not have evidence of recombination with any of the nine human genotypes and four nonhuman genotypes. Based on a comparison of the entire nucleotide sequence against 1,440 HBV isolates reported, HBV/J was nearest to the gibbon and orangutan genotypes (mean divergences of 10.9 and 10.7%, respectively). Based on a comparison of four open reading frames, HBV/J was closer to gibbon/orangutan genotypes than to human genotypes in the P and large S genes and closest to Australian aboriginal strains (HBV/C4) and orangutan-derived strains in the S gene, whereas it was closer to human than ape genotypes in the C gene. HBV/J shared a deletion of 33 nucleotides at the start of preS1 region with C4 and gibbon genotypes, had an S-gene sequence similar to that of C4, and expressed the ayw subtype. Efficient infection, replication, and antigen expression by HBV/J were experimentally established in two chimeric mice with the liver repopulated for human hepatocytes. The HBV DNA sequence recovered from infected mice was identical to that in the inoculum. Since HBV/J is positioned phylogenetically in between human and ape genotypes, it may help to trace the origin of HBV and merits further epidemiological surveys.
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Abstract
Understanding the evolutionary history of human viruses, along with the factors that have shaped their spatial distributions, is one of the most active areas of study in the field of microbial evolution. I give an overview of our current knowledge of the genetic diversity of human viruses using comparative studies of viral populations, particularly those with RNA genomes, to highlight important generalities in the patterns and processes of viral evolution. Special emphasis is given to the major dichotomy between RNA and DNA viruses in their epidemiological dynamics and the different types of phylogeographic pattern exhibited by human viruses. I also consider a central paradox in studies of viral evolution: Although epidemiological theory predicts that RNA viruses have ancestries dating back millennia, with major ecological transitions facilitating their emergence, the genetic diversity in currently circulating viral populations has a far more recent ancestry, indicative of continual lineage turnover.
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Affiliation(s)
- Edward C Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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24
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Postnatal stem/progenitor cells derived from the dental pulp of adult chimpanzee. BMC Cell Biol 2008; 9:20. [PMID: 18430234 PMCID: PMC2383882 DOI: 10.1186/1471-2121-9-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 04/22/2008] [Indexed: 01/01/2023] Open
Abstract
Background Chimpanzee dental pulp stem/stromal cells (ChDPSCs) are very similar to human bone marrow derived mesenchymal stem/stromal cells (hBMSCs) as demonstrated by the expression pattern of cell surface markers and their multipotent differentiation capability. Results ChDPSCs were isolated from an incisor and a canine of a forty-seven year old female chimpanzee. A homogenous population of ChDPSCs was established in early culture at a high proliferation rate and verified by the expression pattern of thirteen cell surface markers. The ChDPSCs are multipotent and were capable of differentiating into osteogenic, adipogenic and chondrogenic lineages under appropriate in vitro culture conditions. ChDPSCs also express stem cell (Sox-2, Nanog, Rex-1, Oct-4) and osteogenic (Osteonectin, osteocalcin, osteopontin) markers, which is comparable to reported results of rhesus monkey BMSCs (rBMSCs), hBMSCs and hDPSCs. Although ChDPSCs vigorously proliferated during the initial phase and gradually decreased in subsequent passages, the telomere length indicated that telomerase activity was not significantly reduced. Conclusion These results demonstrate that ChDPSCs can be efficiently isolated from post-mortem teeth of adult chimpanzees and are multipotent. Due to the almost identical genome composition of humans and chimpanzees, there is an emergent need for defining the new role of chimpanzee modeling in comparative medicine. Teeth are easy to recover at necropsy and easy to preserve prior to the retrieval of dental pulp for stem/stromal cells isolation. Therefore, the establishment of ChDPSCs would preserve and maximize the applications of such a unique and invaluable animal model, and could advance the understanding of cellular functions and differentiation control of adult stem cells in higher primates.
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25
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Yang J, Xi Q, Deng R, Wang J, Hou J, Wang X. Identification of interspecies recombination among hepadnaviruses infecting cross-species hosts. J Med Virol 2007; 79:1741-50. [PMID: 17854046 DOI: 10.1002/jmv.20983] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Members of the family Hepadnaviridae are divided into two genera, Orthohepadnavirus (from mammalian) and Avihepadnavirus (from avian). Recombination had been found to occur among human hepatitis B virus (HBV) strains of different genotypes, or between hepadnavirus strains from human and nonhuman primate. To reach a comparatively complete inspection of interspecies recombination events among hepadnavirus strains from various hosts, 837 hepadnavirus complete genome sequences from human and 112 from animals were analyzed by using fragment typing to scan for potential interspecies recombinants. Further bootscanning and phylogenetic analyses of the potential recombinants revealed six genome sequences as interspecies recombinants. Interspecies recombination events were found to occur among HBV strains from human and nonhuman primates, from gibbons of different genera, from chimpanzee and an unknown host, and between two avian hepadnavirus strains from birds of different subfamilies, which was identified for the first time. HBV interspecies recombinants were found to have recombination hot spots similar to that of human HBV intergenotype recombinants, breakpoints frequently locating near gene boundaries. Interspecies recombination found in this study may alter current views on hepadnavirus host specificity.
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Affiliation(s)
- Jie Yang
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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26
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Makuwa M, Souquière S, Bourry O, Rouquet P, Telfer P, Mauclère P, Kazanji M, Roques P, Simon F. Complete-genome analysis of hepatitis B virus from wild-born chimpanzees in central Africa demonstrates a strain-specific geographical cluster. J Gen Virol 2007; 88:2679-2685. [PMID: 17872519 DOI: 10.1099/vir.0.82992-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In order to determine whether geographical or species clustering accounts for the distribution of hepatitis B virus (HBV) in subspecies of chimpanzees in Africa, four complete chimpanzee HBV (ChHBV) genome sequences were obtained from eight hepatitis B surface antigen-positive wild-born chimpanzees from Cameroon, Republic of Congo and Gabon. The serological profiles of these chimpanzees corresponded to the acute or chronic highly replicative phase of HBV infection, as confirmed by high plasma HBV loads. Analysis of the sequence alignment of 256 aa (S region) from the eight HBV-infected chimpanzees allowed us to determine the HBV amino acid patterns specific to each chimpanzee subspecies and to their geographical origin. Phylogenetic analysis of both the S region and the complete genome confirmed this distinctive clustering of eight novel ChHBV strains within Pan troglodytes. The strong phylogenetic associations of ChHBV sequences with both chimpanzee subspecies and their geographical origin were therefore confirmed.
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Affiliation(s)
- Maria Makuwa
- Centre International de Recherches Médicales de Franceville, Unité de Rétrovirologie et Centre de Primatologie, Franceville, Gabon
| | - Sandrine Souquière
- Centre International de Recherches Médicales de Franceville, Unité de Rétrovirologie et Centre de Primatologie, Franceville, Gabon
| | - Olivier Bourry
- Centre International de Recherches Médicales de Franceville, Unité de Rétrovirologie et Centre de Primatologie, Franceville, Gabon
| | - Pierre Rouquet
- Centre International de Recherches Médicales de Franceville, Unité de Rétrovirologie et Centre de Primatologie, Franceville, Gabon
| | - Paul Telfer
- Centre International de Recherches Médicales de Franceville, Unité de Rétrovirologie et Centre de Primatologie, Franceville, Gabon
| | | | - Mirdad Kazanji
- Centre International de Recherches Médicales de Franceville, Unité de Rétrovirologie et Centre de Primatologie, Franceville, Gabon
| | - Pierre Roques
- Service de Neurologie, Commissariat Energie Atomique, Fontenay aux Roses, France
| | - François Simon
- Hôpital St Louis, Service de Microbiologie, Paris, France
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27
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Devesa M, Pujol FH. Hepatitis B virus genetic diversity in Latin America. Virus Res 2007; 127:177-84. [PMID: 17280734 DOI: 10.1016/j.virusres.2007.01.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 10/20/2006] [Accepted: 01/08/2007] [Indexed: 02/08/2023]
Abstract
Hepatitis B virus (HBV) infection is still a significant health concern in Latin America, where around 11 million persons are infected. Amerindian populations exhibit the highest prevalences of infection in the region. HBV exhibits a degree of variability intermediate between DNA and RNA viruses. This plasticity leads to the generation of several mutants and genotypic variability. Eight HBV genotypes (A-H) have been described, based on a minimum divergence of 8% of the complete genome sequences. HBV genotype F is the most divergent of the HBV genotypes, is autochthonous to South America and is highly predominant in the Northern region of South America. The recently described HBV genotype H is closely related to genotype F and seems to be restricted to Central and North America. Recombination among different HBV strains seems to be frequent, although it has not been described yet between American genotypes. Inside HBV genotype F, four subgenotypes have been described, which exhibit a geographic pattern of distribution. The clinical and biologic importance of the genotypic diversity of HBV is of major concern at the present moment and has been studied in Asia and Europe. In contrast, it is not known whether infection with the American HBV genotypes F and H is associated with a rapid or slow development of disease. The origin of HBV is still an open question. Depending on the model used for the phylogenetic analysis, an Asian or an American origin of HBV has been proposed. By revisiting the genotypic diversity of HBV, an alternative explanation is that human HBV genotypes might have emerged by several zoonotic introductions, both in the Old and the New World.
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Affiliation(s)
- Marisol Devesa
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 21827, Caracas 1020-A, Venezuela.
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28
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Abstract
Hepatitis B virus (HBV) is a member of the hepadnavirus family. Hepadnaviruses can be found in both mammals (orthohepadnaviruses) and birds (avihepadnaviruses). The genetic variability of HBV is very high. There are eight genotypes of HBV and three clades of HBV isolates from apes that appear to be additional genotypes of HBV. Most genotypes are now divided into subgenotypes with distinct virological and epidemiological properties. In addition, recombination among HBV genotypes increases the variability of HBV. This review summarises current knowledge of the epidemiology of genetic variability in hepadnaviruses and, due to rapid progress in the field, updates several recent reviews on HBV genotypes and subgenotypes.
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Affiliation(s)
- Stephan Schaefer
- Abteilung für Virologie, Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universität Rostock, Schillingallee 70, D-18057 Rostock, Germany.
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29
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Yang J, Xing K, Deng R, Wang J, Wang X. Identification of Hepatitis B virus putative intergenotype recombinants by using fragment typing. J Gen Virol 2006; 87:2203-2215. [PMID: 16847116 DOI: 10.1099/vir.0.81752-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Eight hundred and thirty-seven human Hepatitis B virus (HBV) genomes were categorized into pure genotypes and potential intergenotypes, according to their fragment types which were determined based on similarity and phylogenetic analyses of 13 contrived fragments of 250 bp against the corresponding fragments of the consensus sequences of genotypes A-H. Twenty-five intergenotypes, including 171 genomes, were revealed from the potential intergenotype recombinants by phylogenetic analysis of the precisely derived mosaic fragments. Among these, four new intergenotypes were discovered. Many genomes were revealed as putative intergenotype recombinants for the first time. About 87 % of the putative recombinants were B/C (120) and A/D (29) hybrids. The other recombinants comprised A/B/C, A/C, A/E, A/G, C/D, C/F, C/G, C/U (U for unknown genotype) and B/C/U hybrids. Genotypes A and C showed a higher recombination tendency than did other genotypes. The results also demonstrated region priority and breakpoint hot spots in the intergenotype recombination. Recombination breakpoints were found to be concentrated mainly in the vicinity of the DR1 region (nt 1640-1900), the pre S1/S2 region (nt 3150-100), the 3'-end of the C gene (nt 2330-2450) and the 3'-end of the S gene (nt 650-830). These results support the suggestion that intergenotype recombinants may result from co-infection with different genotypes.
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Affiliation(s)
- Jie Yang
- Department of Infectious Diseases, Nanfang Hospital, Guangzhou 510515, People's Republic of China
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | - Ke Xing
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | - Riqiang Deng
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | - Jinwen Wang
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
| | - Xunzhang Wang
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China
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30
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Abstract
Hepatitis B virus (HBV) infection is widely distributed in both human and ape populations throughout the world and is a major cause of human morbidity and mortality. HBV variants are currently classified into the human genotypes A to H and species-associated chimpanzee and gibbon/orangutan groups. To examine the role of recombination in the evolution of HBV, large-scale data retrieval and automated phylogenetic analysis (TreeOrder scanning) were carried out on all available published complete genome sequences of HBV. We detected a total of 24 phylogenetically independent potential recombinants (different genotype combinations or distinct breakpoints), eight of which were previously undescribed. Instances of intergenotype recombination were observed in all human and ape HBV variants, including evidence for a novel gibbon/genotype C recombinant among HBV variants from Vietnam. By recording sequence positions in trees generated from sequential fragments across the genome, violations of phylogeny between trees also provided evidence for frequent intragenotype recombination between members of genotypes A, D, F/H, and gibbon variants but not in B, C, or the Asian B/C recombinant group. In many cases, favored positions for both inter- and intragenotype recombination matched positions of phylogenetic reorganization between the human and ape genotypes, such as the end of the surface gene and the core gene, where sequence relationships between genotypes changed in the TreeOrder scan. These findings provide evidence for the occurrence of past, extensive recombination events in the evolutionary history of the currently classified genotypes of HBV and potentially in changes in its global epidemiology and associations with human disease.
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Affiliation(s)
- Peter Simmonds
- Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom.
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