1
|
Li Y, Wang F, Zhou J, Li L, Song C, Chen E. Optimal Treatment Based on Interferon No Longer Makes Clinical Cure of Chronic Hepatitis B Far Away: An Evidence-Based Review on Emerging Clinical Data. Clin Pharmacol Ther 2024. [PMID: 38686952 DOI: 10.1002/cpt.3287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Chronic hepatitis B (CHB) remains a major global public health problem. The functional cure is the ideal therapeutic target recommended by the latest guidelines, and pursuing a functional cure has become the key treatment end point of current therapy and for upcoming clinical trials. In this review, based on the latest published clinical research evidence, we analyzed the concept and connotation of clinical cures and elaborated on the benefits of clinical cures in detail. Secondly, we have summarized various potential treatment methods for achieving clinical cures, especially elaborating on the latest research progress of interferon-based optimized treatment strategies in achieving clinical cures. We also analyzed which populations can achieve clinical cures and conducted a detailed analysis of relevant virological and serological markers in screening clinical cure advantage populations and predicting clinical cure achievement. In addition, we also introduced the difficulties that may be encountered in the current pursuit of achieving a clinical cure.
Collapse
Affiliation(s)
- Yujing Li
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Fada Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Zhou
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Lanqing Li
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Chengrun Song
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Enqiang Chen
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
2
|
Potter BI, Thijssen M, Trovão NS, Pineda-Peña A, Reynders M, Mina T, Alvarez C, Amini-Bavil-Olyaee S, Nevens F, Maes P, Lemey P, Van Ranst M, Baele G, Pourkarim MR. Contemporary and historical human migration patterns shape hepatitis B virus diversity. Virus Evol 2024; 10:veae009. [PMID: 38361827 PMCID: PMC10868554 DOI: 10.1093/ve/veae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/16/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
Infection by hepatitis B virus (HBV) is responsible for approximately 296 million chronic cases of hepatitis B, and roughly 880,000 deaths annually. The global burden of HBV is distributed unevenly, largely owing to the heterogeneous geographic distribution of its subtypes, each of which demonstrates different severity and responsiveness to antiviral therapy. It is therefore crucial to the global public health response to HBV that the spatiotemporal spread of each genotype is well characterized. In this study, we describe a collection of 133 newly sequenced HBV strains from recent African immigrants upon their arrival in Belgium. We incorporate these sequences-all of which we determine to come from genotypes A, D, and E-into a large-scale phylogeographic study with genomes sampled across the globe. We focus on investigating the spatio-temporal processes shaping the evolutionary history of the three genotypes we observe. We incorporate several recently published ancient HBV genomes for genotypes A and D to aid our analysis. We show that different spatio-temporal processes underlie the A, D, and E genotypes with the former two having originated in southeastern Asia, after which they spread across the world. The HBV E genotype is estimated to have originated in Africa, after which it spread to Europe and the Americas. Our results highlight the use of phylogeographic reconstruction as a tool to understand the recent spatiotemporal dynamics of HBV, and highlight the importance of supporting vulnerable populations in accordance with the needs presented by specific HBV genotypes.
Collapse
Affiliation(s)
- Barney I Potter
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Marijn Thijssen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Nídia Sequeira Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, United States
| | - Andrea Pineda-Peña
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT; Universidade Nova de Lisboa, UNL, Portugal Rua da Junqueira No 100, Lisbon 1349-008, Portugal
- Molecular Biology and Immunology Department, Fundacion Instituto de Inmunología de Colombia (FIDIC); Faculty of Animal Science, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A.), Avenida 50 No. 26-20, Bogota 0609, Colombia
| | - Marijke Reynders
- Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Jan Brugge-Oostende AV, Ruddershove 10, Bruges B-8000, Belgium
| | - Thomas Mina
- Nonis Lab Microbiology—Virology Unit, Gregori Afxentiou 5, Limassol 4003, Cyprus
| | - Carolina Alvarez
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Samad Amini-Bavil-Olyaee
- Cellular Sciences Department, Process Virology, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospital Leuven, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Marc Van Ranst
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Mahmoud Reza Pourkarim
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion, Hemmat Exp.Way, Tehran 14665-1157, Iran
| |
Collapse
|
3
|
Sant'Anna TB, Araujo NM. Hepatitis B Virus Genotype D: An Overview of Molecular Epidemiology, Evolutionary History, and Clinical Characteristics. Microorganisms 2023; 11:1101. [PMID: 37317074 PMCID: PMC10221421 DOI: 10.3390/microorganisms11051101] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 06/16/2023] Open
Abstract
The hepatitis B virus (HBV) genotype D (HBV/D) is the most extensively distributed genotype worldwide with distinct molecular and epidemiological features. This report provides an up-to-date review on the history of HBV/D subgenotyping and misclassifications, along with large-scale analysis of over 1000 HBV/D complete genome sequences, with the aim of gaining a thorough understanding of the global prevalence and geographic distribution of HBV/D subgenotypes. We have additionally explored recent paleogenomic findings, which facilitated the detection of HBV/D genomes dating back to the late Iron Age and provided new perspectives on the origins of modern HBV/D strains. Finally, reports on distinct disease outcomes and responses to antiviral therapy among HBV/D subgenotypes are discussed, further highlighting the complexity of this genotype and the importance of HBV subgenotyping in the management and treatment of hepatitis B.
Collapse
Affiliation(s)
- Thaís B Sant'Anna
- Laboratory of Molecular Virology and Parasitology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21041-250, RJ, Brazil
| | - Natalia M Araujo
- Laboratory of Molecular Virology and Parasitology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21041-250, RJ, Brazil
| |
Collapse
|
4
|
Begg TJA, Schmidt A, Kocher A, Larmuseau MHD, Runfeldt G, Maier PA, Wilson JD, Barquera R, Maj C, Szolek A, Sager M, Clayton S, Peltzer A, Hui R, Ronge J, Reiter E, Freund C, Burri M, Aron F, Tiliakou A, Osborn J, Behar DM, Boecker M, Brandt G, Cleynen I, Strassburg C, Prüfer K, Kühnert D, Meredith WR, Nöthen MM, Attenborough RD, Kivisild T, Krause J. Genomic analyses of hair from Ludwig van Beethoven. Curr Biol 2023; 33:1431-1447.e22. [PMID: 36958333 DOI: 10.1016/j.cub.2023.02.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/11/2022] [Accepted: 02/13/2023] [Indexed: 03/25/2023]
Abstract
Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.
Collapse
Affiliation(s)
- Tristan James Alexander Begg
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
| | - Axel Schmidt
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany
| | - Arthur Kocher
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Maarten H D Larmuseau
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Laboratory of Human Genetic Genealogy, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ARCHES - Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, 2000 Antwerp, Belgium; Histories vzw, 9000 Gent, Belgium
| | | | | | - John D Wilson
- Austrian Academy of Sciences, 1030 Vienna, Austria; University of Vienna, 1010 Vienna, Austria
| | - Rodrigo Barquera
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Carlo Maj
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany; Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - András Szolek
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | | | - Stephen Clayton
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Alexander Peltzer
- Quantitative Biology Center (QBiC) University of Tübingen, Tübingen, Germany
| | - Ruoyun Hui
- MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; Alan Turing Institute, 2QR, John Dodson House, London NW1 2DB, UK
| | | | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - Cäcilia Freund
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Marta Burri
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Franziska Aron
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Anthi Tiliakou
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Joanna Osborn
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Guido Brandt
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Isabelle Cleynen
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Christian Strassburg
- Department of Internal Medicine I, University Hospital Bonn, 53127 Bonn, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - William Rhea Meredith
- American Beethoven Society, San Jose State University, San Jose, CA 95192, USA; Ira F. Brilliant Center for Beethoven Studies, San Jose State University, San Jose, CA 95192, USA; School of Music and Dance, San Jose State University, San Jose, CA 95192, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany
| | - Robert David Attenborough
- MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; School of Archaeology & Anthropology, Australian National University, Canberra, ACT 0200, Australia
| | - Toomas Kivisild
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
| |
Collapse
|
5
|
Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals. Viruses 2023; 15:v15020458. [PMID: 36851671 PMCID: PMC9964524 DOI: 10.3390/v15020458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
The study aimed to characterize the genotype and subgenotypes of HBV circulating in Saudi Arabia, the presence of clinically relevant mutations possibly associated with resistance to antivirals or immune escape phenomena, and the possible impact of mutations in the structural characteristics of HBV polymerase. Plasma samples from 12 Saudi Arabian HBV-infected patients were analyzed using an in-house PCR method and direct sequencing. Saudi patients were infected with mainly subgenotype D1. A number of mutations in the RT gene (correlated to antiviral resistance) and within and outside the major hydrophilic region of the S gene (claimed to influence immunogenicity and be related to immune escape) were observed in almost all patients. Furthermore, the presence of mutations in the S region caused a change in the tertiary structure of the protein compared with the consensus region. Clinical manifestations of HBV infection may change dramatically as a result of viral and host factors: the study of mutations and protein-associated cofactors might define possible aspects relevant for the natural and therapeutic history of HBV infection.
Collapse
|
6
|
Trovão NS, Thijssen M, Vrancken B, Pineda-Peña AC, Mina T, Amini-Bavil-Olyaee S, Lemey P, Baele G, Pourkarim MR. Reconstruction of the Origin and Dispersal of the Worldwide Dominant Hepatitis B Virus Subgenotype D1. Virus Evol 2022; 8:veac028. [PMID: 35712523 PMCID: PMC9194798 DOI: 10.1093/ve/veac028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 12/01/2022] Open
Abstract
Hepatitis B is a potentially life-threatening liver infection caused by the hepatitis B virus (HBV). HBV-D1 is the dominant subgenotype in the Mediterranean basin, Eastern Europe, and Asia. However, little is currently known about its evolutionary history and spatio-temporal dynamics. We use Bayesian phylodynamic inference to investigate the temporal history of HBV-D1, for which we calibrate the molecular clock using ancient sequences, and reconstruct the viral global spatial dynamics based, for the first time, on full-length publicly available HBV-D1 genomes from a wide range of sampling dates. We pinpoint the origin of HBV subgenotype D1 before the current era (BCE) in Turkey/Anatolia. The spatial reconstructions reveal global viral transmission with a high degree of mixing. By combining modern-day and ancient sequences, we ensure sufficient temporal signal in HBV-D1 data to enable Bayesian phylodynamic inference using a molecular clock for time calibration. Our results shed light on the worldwide HBV-D1 epidemics and suggest that this originally Middle Eastern virus significantly affects more distant countries, such as those in mainland Europe.
Collapse
Affiliation(s)
- Nídia Sequeira Trovão
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Marijn Thijssen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Andrea-Clemencia Pineda-Peña
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT; Universidade Nova de Lisboa, UNL, Lisbon, Portugal Rua da Junqueira No 100, 1349-008, Lisbon, Portugal
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC); Faculty of Animal Science, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Avenida 50 No. 26-20 Bogotá, Colombia
| | - Thomas Mina
- Mina Clinical Laboratory, Gregori Afxentiou, Iocasti Court Block A, Flat 22 Mesa Yitonia, 4003 Lemesos, Cyprus
| | - Samad Amini-Bavil-Olyaee
- Biosafety Development Group, Cellular Sciences Department, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium, Herestraat 49, BE-3000 Leuven, Belgium
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Hemmat Exp. Way, 14665-1157, Tehran, Iran
| |
Collapse
|
7
|
Belyhun Y, Liebert UG, Maier M. Molecular epidemiology of hepatitis B virus among HIV co-infected and mono-infected cohorts in Northwest Ethiopia. Virol J 2022; 19:53. [PMID: 35331278 PMCID: PMC8944073 DOI: 10.1186/s12985-022-01774-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is a particular concern in human immunodeficiency virus (HIV) infected individuals. In Ethiopia, detailed clinical and virological descriptions of HBV prevailing during HIV co-infection and symptomatic liver disease patients are lacking. The aim of this study was to investigate HBV virological characteristics from Ethiopian HBV/HIV co-infected and HBV mono-infected individuals. METHODS A total of 4105 sera from HIV positive individuals, liver disease patients, and blood donors were screened serologically for HBV. The overlapping polymerase/surface genome region of HBV from 180 infected individuals was extracted, amplified, and sequenced for genotypic analysis. RESULTS The HBsAg seroprevalence was detected 43% in liver disease patients, 8.4% in blood donors, and 6.7% in HIV/HBV co-infected individuals. The occult HBV prevalence was 3.7% in HIV/HBV co-infected individuals and 2.8% in blood donors with an overall prevalence rate of 3.4%. A phylogenetic analysis showed three HBV genotypes; A (61.1%), D (38.3%) and E (0.6%). Genotype A belongs to subtypes A1 (99.1%) and A9 (0.9%), but genotype D showed heterogeneous subtypes; D2 (63.8%) followed by D4 (21.7%), D1 (8.7%), D3 (4.3%), and D10 (1.4%). CONCLUSIONS The HIV/HBV co-infected individuals and blood donors showed lower HBsAg seroprevalence compared to liver diseases patients. Occult HBV prevalence showed no difference between HIV/HBV co-infected and blood donor groups. This study demonstrated predominance distribution of HBV subtypes A1 and D2 in northwest Ethiopia. The observed virological characteristics could contribute for evidence-based management of viral hepatitis in Ethiopia where antiretroviral therapy guidelines do not cater for viral hepatitis screening during HIV co-infection.
Collapse
Affiliation(s)
- Yeshambel Belyhun
- Department of Virology, Institute of Medical Microbiology, Leipzig University, Leipzig, Germany. .,School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
| | - Uwe Gerd Liebert
- Department of Virology, Institute of Medical Microbiology, Leipzig University, Leipzig, Germany
| | - Melanie Maier
- Department of Virology, Institute of Medical Microbiology, Leipzig University, Leipzig, Germany
| |
Collapse
|
8
|
Athamneh RY, Arıkan A, Sayan M, Mahafzah A, Sallam M. Variable Proportions of Phylogenetic Clustering and Low Levels of Antiviral Drug Resistance among the Major HBV Sub-Genotypes in the Middle East and North Africa. Pathogens 2021; 10:1333. [PMID: 34684283 PMCID: PMC8540944 DOI: 10.3390/pathogens10101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022] Open
Abstract
Hepatitis B virus (HBV) infection remains a major public health threat in the Middle East and North Africa (MENA). Phylogenetic analysis of HBV can be helpful to study the putative transmission links and patterns of inter-country spread of the virus. The objectives of the current study were to analyze the HBV genotype/sub-genotype (SGT) distribution, reverse transcriptase (RT), and surface (S) gene mutations and to investigate the domestic transmission of HBV in the MENA. All HBV molecular sequences collected in the MENA were retrieved from GenBank as of 30 April 2021. Determination of genotypes/SGT, RT, and S mutations were based on the Geno2pheno (hbv) 2.0 online tool. For the most prevalent HBV SGTs, maximum likelihood phylogenetic analysis was conducted to identify the putative phylogenetic clusters, with approximate Shimodaira-Hasegawa-like likelihood ratio test values ≥ 0.90, and genetic distance cut-off values ≤ 0.025 substitutions/site as implemented in Cluster Picker. The total number of HBV sequences used for genotype/SGT determination was 4352 that represented a total of 20 MENA countries, with a majority from Iran (n = 2103, 48.3%), Saudi Arabia (n = 503, 11.6%), Tunisia (n = 395, 9.1%), and Turkey (n = 267, 6.1%). Genotype D dominated infections in the MENA (86.6%), followed by genotype A (4.1%), with SGT D1 as the most common in 14 MENA countries and SGT D7 dominance in the Maghreb. The highest prevalence of antiviral drug resistance was observed against lamivudine (4.5%) and telbivudine (4.3%). The proportion of domestic phylogenetic clustering was the highest for SGT D7 (61.9%), followed by SGT D2 (28.2%) and genotype E (25.7%). The largest fraction of domestic clusters with evidence of inter-country spread within the MENA was seen in SGT D7 (81.3%). Small networks (containing 3-14 sequences) dominated among domestic phylogenetic clusters. Specific patterns of HBV genetic diversity were seen in the MENA with SGT D1 dominance in the Levant, Iran, and Turkey; SGT D7 dominance in the Maghreb; and extensive diversity in Saudi Arabia and Egypt. A low prevalence of lamivudine, telbivudine, and entecavir drug resistance was observed in the region, with almost an absence of resistance to tenofovir and adefovir. Variable proportions of phylogenetic clustering indicated prominent domestic transmission of SGT D7 (particularly in the Maghreb) and relatively high levels of virus mobility in SGT D1.
Collapse
Affiliation(s)
- Rabaa Y. Athamneh
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (R.Y.A.); (A.A.)
| | - Ayşe Arıkan
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (R.Y.A.); (A.A.)
- DESAM, Near East University, Nicosia 99138, Cyprus;
| | - Murat Sayan
- DESAM, Near East University, Nicosia 99138, Cyprus;
- Clinical Laboratory, PCR Unit, Faculty of Medicine, Kocaeli University, İzmit 41380, Turkey
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Amman 11942, Jordan;
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Amman 11942, Jordan;
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22184 Malmö, Sweden
| |
Collapse
|
9
|
Abdullahi IN, Emeribe AU, Ghamba PE, Omosigho PO, Bello ZM, Oderinde BS, Fasogbon SA, Olayemi L, Daneji IM, Musa MH, Nwofe JO, Onukegbe NB, Okume CC, Musa S, Gwarzo AM, Ajagbe OOR. Distribution pattern and prevalence of West Nile virus infection in Nigeria from 1950 to 2020: a systematic review. Epidemiol Health 2020; 42:e2020071. [PMID: 33254358 PMCID: PMC8137371 DOI: 10.4178/epih.e2020071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES West Nile virus (WNV) is a re-emerging mosquito-borne viral infection. This study investigated the pooled prevalence pattern and risk factors of WNV infection among humans and animals in Nigeria. METHODS A systematic review was conducted of eligible studies published in PubMed, Scopus, Google Scholar, and Web of Science from January 1, 1950 to August 30, 2020. Peer-reviewed cross-sectional studies describing WNV infections in humans and animals were systematically reviewed. Heterogeneity was assessed using the Cochrane Q statistic. RESULTS Eighteen out of 432 available search output were eligible and included for this study. Of which 13 and 5 were WNV studies on humans and animals, respectively. Although 61.5% of the human studies had a low risk of bias, they all had high heterogeneity. The South West geopolitical zone of Nigeria had the highest pooled prevalence of anti-WNV immunoglobulin M (IgM; 7.8% in humans). The pooled seroprevalence of anti-WNV IgM and immunoglobulin G (IgG) was 7.1% (95% confidence interval [CI], 5.9 to 8.3) and 76.5% (95% CI, 74.0 to 78.8), respectively. The WNV RNA prevalence was 1.9% (95% CI, 1.4 to 2.9), while 14.3% (95% CI, 12.9 to 15.8) had WNV-neutralizing antibodies. In animals, the pooled seroprevalence of anti-WNV IgM and IgG was 90.3% (95% CI, 84.3 to 94.6) and 3.5% (95% CI, 1.9 to 5.8), respectively, while 20.0% (95% CI, 12.9 to 21.4) had WNV-neutralizing antibodies. Age (odds ratio [OR], 3.73; 95% CI, 1.87 to 7.45; p<0.001) and level of education (no formal education: OR, 4.31; 95% CI, 1.08 to 17.2; p<0.05; primary: OR, 7.29; 95% CI, 1.80 to 29.6; p<0.01) were significant risk factors for WNV IgM seropositivity in humans. CONCLUSIONS The findings of this study highlight the endemicity of WNV in animals and humans in Nigeria and underscore the need for the One Health prevention and control approach.
Collapse
Affiliation(s)
- Idris Nasir Abdullahi
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Anthony Uchenna Emeribe
- Department of Medical Laboratory Science, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | - Peter Elisha Ghamba
- WHO National Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | | | - Zakariyya Muhammad Bello
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Bamidele Soji Oderinde
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Maiduguri, Maiduguri, Nigeria
| | - Samuel Ayobami Fasogbon
- Public Health In-vitro Diagnostic Control Laboratory, Medical Laboratory Science Council of Nigeria, Lagos, Nigeria
| | - Lawal Olayemi
- Department of Medicine, National University of Samoa, Samoa
| | - Isa Muhammad Daneji
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University, Kano, Nigeria
| | - Muhammad Hamis Musa
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University, Kano, Nigeria
| | | | | | - Chukwudi Crescent Okume
- Department of Medical Laboratory Service, University of Nigeria Teaching Hospital, Enugu, Nigeria
| | - Sanusi Musa
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Ahmadu Bello University, Zaria, Nigeria
| | | | | |
Collapse
|
10
|
Neukamm J, Pfrengle S, Molak M, Seitz A, Francken M, Eppenberger P, Avanzi C, Reiter E, Urban C, Welte B, Stockhammer PW, Teßmann B, Herbig A, Harvati K, Nieselt K, Krause J, Schuenemann VJ. 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC Biol 2020; 18:108. [PMID: 32859198 PMCID: PMC7456089 DOI: 10.1186/s12915-020-00839-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging. RESULTS The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed. CONCLUSIONS The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.
Collapse
Affiliation(s)
- Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Alexander Seitz
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Michael Francken
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Partick Eppenberger
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, USA
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Christian Urban
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Beatrix Welte
- Institute of Pre- and Protohistory and Medieval Archaeology, Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Philipp W Stockhammer
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799, Munich, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Barbara Teßmann
- Berlin Society of Anthropology, Ethnology and Prehistory, 10117, Berlin, Germany.,Museum of Prehistory and Early History, SMPK Berlin, 10117, Berlin, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Katerina Harvati
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,DFG Centre for Advanced Studies Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.
| |
Collapse
|
11
|
Tracing back hepatitis B virus genotype D introduction and dissemination in South Brazil. INFECTION GENETICS AND EVOLUTION 2020; 82:104294. [DOI: 10.1016/j.meegid.2020.104294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/04/2020] [Accepted: 03/22/2020] [Indexed: 12/14/2022]
|
12
|
McNaughton AL, Revill PA, Littlejohn M, Matthews PC, Ansari MA. Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences. J Gen Virol 2020; 101:271-283. [PMID: 32134374 PMCID: PMC7416611 DOI: 10.1099/jgv.0.001387] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online (https://doi.org/10.6084/m9.figshare.8851946) as a simple open-access resource.
Collapse
Affiliation(s)
- Anna L. McNaughton
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Peter A. Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Philippa C. Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - M. Azim Ansari
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| |
Collapse
|
13
|
Bruni R, Villano U, Taffon S, Equestre M, Madonna E, Chionne P, Candido A, Dettori S, Pisani G, Rapicetta M, Bortolotti F, Ciccaglione AR. Retrospective analysis of acute HBV infections occurred in 1978-79 and 1994-95 in North-East Italy: increasing prevalence of BCP/pre-core mutants in sub-genotype D3. BMC Infect Dis 2020; 20:78. [PMID: 31992230 PMCID: PMC6988336 DOI: 10.1186/s12879-019-4713-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/18/2019] [Indexed: 11/21/2022] Open
Abstract
Background At the end of the 1970s, in Italy more than 2% of the general population was HBsAg carrier. In the late ‘70s and late ‘80s, two remarkable events might have impacted on HBV strains transmitted in North-East Italy: (a) the increased HBV incidence due to parenteral drugs between 1978 and 1982; (b) the preventive anti-HIV educational campaign, started locally in 1985. Methods To address if those events impacted on circulating HBV variants, acute cases occurred in North-East Italy in 1978–79 (n = 50) and 1994–95 (n = 30) were retrospectively analysed. HBV sequences obtained from serum samples were subjected to phylogenetic analysis and search for BCP/pre-core and S mutations. Results HBV-D was the most prevalent genotype in both 1978–79 (43/50, 86%) and 1994–95 (24/30, 80.0%), with HBV-A in all but one remaining cases. Among HBV-D cases, sub-genotype HBV-D3 was the most prevalent (25/29, 86.2% in 1978–79; 13/16, 81.2% in 1994–95), with HBV-D1 and HBV-D2 in the remaining cases. All HBV-A cases were sub-genotype A2. Single and multiple BCP/pre-core mutations, responsible for HBeAg(−) hepatitis, were detected in 6/50 (12%) cases in 1978/79 vs. 12/30 (40.0%) in 1994/95 (p = 0.006). They were found exclusively in HBV-D; in the most abundant sub-genotype, HBV-D3, they were detected in 2/25 (8%) cases in 1978–79 vs. 6/13 (46%) in 1994–95 (p = 0.011). No vaccine escape S mutations were observed. The IDU risk factor was significantly more frequent in 1994–95 (8/30, 26.7%) than in 1978–79 (4/50, 8%) (p = 0.048). Conclusions The above mentioned epidemiological and public health events did not affect the proportion of genotypes and sub-genotypes that remained unchanged over 16 years. In contrast, the proportion of BCP/pre-core mutants increased more than three-fold, mostly in HBV-D3, a sub-genotype highly circulating in IDUs; drug abuse likely contributed to the spread of these mutants. The findings contribute to explain a previously described major change in HBV epidemiology in Italy: the proportion of HBeAg(−) cases in the carrier cohort changed from low in late 1970s, to high at the beginning of the 2000s. In addition to other recognized factors, the increased circulation of BCP/pre-core mutants likely represents a further factor that contributed to this change.
Collapse
Affiliation(s)
- Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Umbertina Villano
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stefania Taffon
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Michele Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Madonna
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Chionne
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Angela Candido
- Notified Body 0373, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Dettori
- Notified Body 0373, Istituto Superiore di Sanità, Rome, Italy
| | - Giulio Pisani
- National Centre for the Control and Evaluation of Medicines, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Rapicetta
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Flavia Bortolotti
- Department of Experimental and Clinical Medicine, University of Padua, Padua, Italy
| | | |
Collapse
|
14
|
Al-Qahtani AA, Pourkarim MR, Trovão NS, Vergote V, Li G, Thijssen M, Abdo AA, Sanai FM, Dela Cruz D, Bohol MFF, Al-Anazi MR, Al-Ahdal MN. Molecular epidemiology, phylogenetic analysis and genotype distribution of hepatitis B virus in Saudi Arabia: Predominance of genotype D1. INFECTION GENETICS AND EVOLUTION 2019; 77:104051. [PMID: 31634640 DOI: 10.1016/j.meegid.2019.104051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/28/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023]
Abstract
Despite the implementation of various vaccination programs, hepatitis B virus (HBV) poses a considerable health problem in Saudi Arabia. Insight on HBV evolutionary history in the region is limited. We performed a comprehensive epidemiological and phylogenetic reconstruction based on a large cohort of HBV infected patients. Three hundred and nineteen HBV-infected patients with different clinical manifestations, including inactive and active chronic carriers and patients with cirrhosis and hepatocellular carcinoma (HCC), were enrolled in this study. The full-length large S gene was amplified and sequenced. Phylogenetic analysis was performed to determine the genotype and subgenotypes of the isolates. Phylogenetic tree analysis revealed that genotype D is the most dominant genotype among patients. Moreover, this analysis identified two strains with genotype E isolated from active carriers. Detailed phylogenetic analyses confirmed the presence of four HBV D subgenotypes, D1 (93%, n = 296), D2 (0.02%, n = 5), D3 (0.003%, n = 1), and D4 (0.003%, n = 1). In addition, six genotype D strains were not assigned to any existing HBV D subgenotype. The large S gene of eight strains showed signatures of genotype recombination between the genotypes D and A and between D and E. Several strains harbored medically important point mutations at the protein level. Along with the dominance of the HBV genotype D, isolation of the E genotype and several recombinant strains from patients with Saudi Arabian origin is an essential result for decisions involving therapeutic measures for patients. Development of vaccines and detection of diagnostic escape mutations at antigenic epitopes on the HBsAg will be valuable to public health authorities. Furthermore, the diversity at the nucleotide and amino acid levels and different proportions of dN/dS at the PreS1, PreS2, and HBsAg reveal the selective pressure trend from inactive status towards advanced liver diseases.
Collapse
Affiliation(s)
- Ahmed A Al-Qahtani
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Department of Microbiology and Immunology, Alfaisal University, School of Medicine, Riyadh, Saudi Arabia.
| | - Mahmoud Reza Pourkarim
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Nídia Sequeira Trovão
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Guangdi Li
- Department of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Marijn Thijssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Ayman A Abdo
- Section of Gastroenterology, Department of Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Faisal M Sanai
- Gastroenterology Unit, Department of Medicine, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Damian Dela Cruz
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Marie Fe F Bohol
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mashael R Al-Anazi
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mohammed N Al-Ahdal
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Department of Microbiology and Immunology, Alfaisal University, School of Medicine, Riyadh, Saudi Arabia
| |
Collapse
|
15
|
Reconstruction of the spatial and temporal dynamics of hepatitis B virus genotype D in the Americas. PLoS One 2019; 14:e0220342. [PMID: 31344111 PMCID: PMC6657902 DOI: 10.1371/journal.pone.0220342] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/13/2019] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B virus (HBV) genotype D (HBV/D) is globally widespread, and ten subgenotypes (D1 to D10) showing distinct geographic distributions have been described to date. The evolutionary history of HBV/D and its subgenotypes, for which few complete genome sequences are available, in the Americas is not well understood. The main objective of the current study was to determine the full-length genomic sequences of HBV/D isolates from Brazil and frequency, origin and spread of HBV/D subgenotypes in the Americas. Complete HBV/D genomes isolated from 39 Brazilian patients infected with subgenotypes D1 (n = 1), D2 (n = 10), D3 (n = 27), and D4 (n = 1) were sequenced and analyzed together with reference sequences using the Bayesian coalescent and phylogeographic framework. A search for HBV/D sequences available in GenBank revealed 209 complete and 926 partial genomes from American countries (Argentina, Brazil, Canada, Chile, Colombia, Cuba, Haiti, Martinique, Mexico, USA and Venezuela), with the major circulating subgenotypes identified as D1 (26%), D2 (17%), D3 (36%), D4 (21%), and D7 (1%) within the continent. The detailed evolutionary history of HBV/D in the Americas was investigated by using different evolutionary time scales. Spatiotemporal reconstruction analyses using short-term substitution rates suggested times of the most recent common ancestor for the American HBV/D subgenotypes coincident with mass migratory movements to Americas during the 19th and 20th centuries. In particular, significant linkages between Argentina and Syria (D1), Brazil and Central/Eastern Europe (D2), USA and India (D2), and Brazil and Southern Europe (D3) were estimated, consistent with historical and epidemiological data.
Collapse
|
16
|
Sagnelli C, Pisaturo M, Calò F, Martini S, Sagnelli E, Coppola N. Reactivation of hepatitis B virus infection in patients with hemo-lymphoproliferative diseases, and its prevention. World J Gastroenterol 2019; 25:3299-3312. [PMID: 31341357 PMCID: PMC6639550 DOI: 10.3748/wjg.v25.i26.3299] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/10/2019] [Accepted: 05/18/2019] [Indexed: 02/06/2023] Open
Abstract
Reactivation of hepatitis B virus (HBV) replication is characterized by increased HBV-DNA serum values of about 1 log or by HBV DNA turning positive if previously undetectable in serum, possibly associated with liver damage and seldom life-threatening. Due to HBV reactivation, hepatitis B surface antigen (HBsAg)-negative/anti-HBc-positive subjects may revert to HBsAg-positive. In patients with hemo-lymphoproliferative disease, the frequency of HBV reactivation depends on the type of lymphoproliferative disorder, the individual's HBV serological status and the potency and duration of immunosuppression. In particular, it occurs in 10%-50% of the HBsAg-positive and in 2%-25% of the HBsAg- negative/anti-HBc-positive, the highest incidences being registered in patients receiving rituximab-based therapy. HBV reactivation can be prevented by accurate screening of patients at risk and by a pharmacological prophylaxis with anti-HBV nucleo(t)sides starting 2-3 wk before the beginning of immunosuppressive treatment and covering the entire period of administration of immunosuppressive drugs and a long subsequent period, the duration of which depends substantially on the degree of immunodepression achieved. Patients with significant HBV replication before immunosuppressive therapy should receive anti-HBV nucleo(t)sides as a long-term (may be life-long) treatment. This review article is mainly directed to doctors engaged every day in the treatment of patients with onco-lymphoproliferative diseases, so that they can broaden their knowledge on HBV infection and on its reactivation induced by the drugs with high immunosuppressive potential that they use in the care of their patients.
Collapse
Affiliation(s)
- Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples 80127, Italy
| | - Mariantonietta Pisaturo
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples 80127, Italy
| | - Federica Calò
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples 80127, Italy
| | - Salvatore Martini
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples 80127, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples 80127, Italy
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples 80127, Italy
| |
Collapse
|
17
|
Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review. J Med Virol 2019; 91:1707-1724. [PMID: 31243773 DOI: 10.1002/jmv.25526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022]
Abstract
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
Collapse
Affiliation(s)
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Roma, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| |
Collapse
|
18
|
Mojsiejczuk L, Elizalde MM, López G, Figueredo D, Marquez N, Campos RH, Flichman D. Molecular epidemiology of hepatitis B virus in Paraguay. INFECTION GENETICS AND EVOLUTION 2019; 71:91-97. [PMID: 30910532 DOI: 10.1016/j.meegid.2019.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 12/18/2022]
Abstract
Hepatitis B virus (HBV) infection is a leading cause of severe chronic liver disease worldwide. The HBV epidemiology in Latin American countries is complex and the data is still scanty and fragmentary. The aim of this study was to investigate the distribution of HBV genotypes in Paraguay and to estimate the viral population dynamic and spread pattern of the main phylogenetic group. To this end, partial and complete genome sequences were obtained from 60 blood donor candidates and analysed by phylogenetic and Bayesian phylodynamic approaches. The phylogenetic analysis based on sequences of partial Polymerase/Pre-S1 overlapping region showed a predominance of the Native American subgenotype F4 (81.7%), the presence of the European subgenotypes A2 (1.7%) and D3 (8.3%), the African subgenotype A1 (3, 5%) and the Asian subgenotypes B2 (1.7%) and C2 (1.7%). The distribution of HBV genotypes was in accordance with the ethnic composition of the population. The phylogeographic analysis of subgenotype F4 complete genomes suggests that this lineage emerged and spread in the last 300 years. Paraguay was the most probable location of the common ancestor. The lineage diverged into two main clades and spread to neighbor regions, mainly Bolivia and Northwest Argentina, and Buenos Aires. The phylogeny showed a scanty geographical structure and a complex migratory pattern. In conclusion, the HBV genotypes circulating in Paraguay reflect the ethnic origin of the population. The distribution of genotypes and the phylogeographic reconstruction showed the impact of both global and local migrations in shaping the HBV molecular epidemiology in the region.
Collapse
Affiliation(s)
- Laura Mojsiejczuk
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Virología, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Mercedes Elizalde
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Virología, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Gladys López
- Laboratorio de Referencia del Programa Nacional de Control de VIH y otras ITS, Ministerio de Salud Pública y Bienestar Social. Avda. Pettirossi esq. Brasil, Asunción, Paraguay
| | - Diego Figueredo
- Red Nacional de Servicios de Sangre del Programa Nacional de Sangre, Ministerio de Salud Pública y Bienestar Social. Avda. Pettirossi esq. Brasil, Asunción, Paraguay
| | - Nelson Marquez
- Red Nacional de Servicios de Sangre del Programa Nacional de Sangre, Ministerio de Salud Pública y Bienestar Social. Avda. Pettirossi esq. Brasil, Asunción, Paraguay
| | - Rodolfo Héctor Campos
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Virología, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Diego Flichman
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Virología, Junín 956 4to piso, Ciudad Autónoma de Buenos Aires, Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| |
Collapse
|
19
|
Epidemiology of West Nile Virus in the Eastern Mediterranean region: A systematic review. PLoS Negl Trop Dis 2019; 13:e0007081. [PMID: 30695031 PMCID: PMC6368338 DOI: 10.1371/journal.pntd.0007081] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 02/08/2019] [Accepted: 12/14/2018] [Indexed: 01/01/2023] Open
Abstract
Background West Nile Virus (WNV), a member of the genus Flavivirus, is one of the most widely distributed arboviruses in the world. Despite some evidence for circulation of WNV in countries summarized by the World Health Organization as the Eastern Mediterrian Regional Office (EMRO), comprehensive knowledge about its epidemiology remains largely unknown. This study aims to provide a concise review of the published literature on WNV infections in the Eastern Mediterranean Regional Office of WHO (EMRO). Methodology/principal findings A systematic review of WNV prevalence studies on humans, animals and vectors in the EMRO region was performed by searching: Web of Science, Science Direct, Scopus, PubMed, Embase and Google Scholar. Finally, 77 citations were included, comprising 35 seroprevalence studies on general population (24460 individuals), 15 prevalence studies among patients (3439 individuals), 22 seroprevalence studies among animals (10309 animals), and 9 studies on vectors (184242 vector species). Of the 22 countries in this region, five had no data on WNV infection among different populations. These countries include Kuwait, Bahrain, Oman, Syria and Somalia. On the other hand, among countries with available data, WNV-specific antibodies were detected in the general population of all investigated countries including Djibouti (0.3–60%), Egypt (1–61%), Iran (0–30%), Iraq (11.6–15.1%), Jordan (8%), Lebanon (0.5–1%), Libya (2.3%), Morocco (0–18.8%), Pakistan (0.6–65.0%), Sudan (2.2–47%), and Tunisia (4.3–31.1%). WNV RNA were also detected in patient populations of Iran (1.2%), Pakistan (33.3%), and Tunisia (5.3% –15.9%). WNV-specific antibodies were also detected in a wide range of animal species. The highest seropositivity rate was observed among equids (100% in Morocco) and dogs (96% in Morocco). The highest seroprevalence among birds was seen in Tunisia (23%). In addition, WNV infection was detected in mosquitoes (Culex, and Aedes) and ticks (Argas reflexus hermanni). The primary vector of WNV (Culex pipiens s.l.) was detected in Djibouti, Egypt, Iran and Tunisia, and in mosquitoes of all these countries, WNV was demonstrated. Conclusions This first systematic regional assessment of WNV prevalence provides evidence to support the circulation of WNV in the EMRO region as nearly all studies showed evidence of WNV infection in human as well as animal/vector populations. These findings highlight the need for continued prevention and control strategies and the collection of epidemiologic data for WNV epidemic status, especially in countries that lack reliable surveillance systems. West Nile Virus (WNV) is a mosquito-borne Flavivirus belonging to the Flaviviridae family, which is endemic in a vast geographical area, including the EMRO region. However, the epidemiology of WNV in the EMRO region remains poorly understood. To address this gap, we performed a systematic review on WNV prevalence studies conducted on human populations, animals and vectors across Eastern Mediterranean countries. Our review indicated the infection of most investigated human, animal and vector populations with WNV; however, the paucity of epidemiological data underline the need for integrated surveillance programs as well as continued deployment of prevention and control strategies.
Collapse
|
20
|
Torres MC, Civetta E, D'amico C, Barbini L. Hepatitis B virus in Mar del Plata, Argentina: Genomic characterization and evolutionary analysis of subgenotype F1b. J Med Virol 2019; 91:791-802. [PMID: 30570771 DOI: 10.1002/jmv.25383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/14/2018] [Indexed: 11/07/2022]
Abstract
The aim is to describe the molecular epidemiology and perform a genomic characterization of hepatitis B virus (HBV) circulating in Mar del Plata and to identify the origin and diversification patterns of the most prevalent genotype. The S gene and the region encompassing the X gene, basal core promoter (BCP), and precore (preC) was analyzed in 56 samples. They were genotyped as: 80% F1b, 9% A2, 7% D3, and 2% D1. A recombinant F4/D2 genome was detected. The double substitution G1764A/A1762T at the BCP (reduced HBeAg expression) was found in 20% F1b, 2% A2, 2% D1, and 2% D3 samples. A unique D3 presented the G1896A substitution at the preC (HBeAg negative phenotype). A 13% of the samples showed mutations at the HBsAg "a" immunodeterminant (escape from neutralizing antibodies). Mutations at the polymerase (antiviral resistance) were found in 52% of the samples. Coalescent analysis of subgenotype F1b, the most prevalent in the city, showed that viral diversification in Mar del Plata started by year 2000. F1b was the most prevalent genotype detected, being a characteristic of actual HBV infections in Mar del Plata. Local HBV exhibit clinically relevant mutations, but a minority of them was shown to be associated to potential vaccination escape or antiviral resistance. Nevertheless, further studies are needed to determine whether any of these mutants could pose a threat to prevention, diagnosis, or treatment.
Collapse
Affiliation(s)
| | - Elida Civetta
- Unidad de Hepatología y Alcoholismo, HIGA Dr. O. Alende, Mar del Plata, Argentina
| | - Claudia D'amico
- Centro de Especialidades Médicas Ambulatorias, Unidad de Hepatología, Mar del Plata, Argentina
| | - Luciana Barbini
- Departamento de Química, FCEyN, UNMdP, Buenos Aires, Argentina
| |
Collapse
|
21
|
Daw MA, Buktir Ali LA, Daw AM, Sifennasr NEM, Dau AA, Agnan MM, El-Bouzedi A. The geographic variation and spatiotemporal distribution of hepatitis C virus infection in Libya: 2007-2016. BMC Infect Dis 2018; 18:594. [PMID: 30466399 PMCID: PMC6251168 DOI: 10.1186/s12879-018-3471-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/31/2018] [Indexed: 02/14/2023] Open
Abstract
BACKGROUND Hepatitis C Virus infection has been considered an important hidden pandemic in developing countries, particularly in Africa. It varies greatly from one region to another and even within districts of the same region. Macroscopic geospatial analysis has become an important scientific tool for identifying the density and clustering of HCV infection and provides epidemiological information for planning interventions and control strategies. The application of these parameters provides a better knowledge of the hepatitis C virus infection prevalence at the national level and can help to implement pertinent strategies to address the HCV-related burdens. This study aims to determine the geographical variability of HCV infection in Libya and to identify the hot spots within regions and districts of the country, and to analyze the population-based demographic determinants involved and outline the intervention programs needed. METHODS Disease mapping and spatial analysis were conducted using geographic information data available on all documented cases of HCV infections in Libya between 2007 and 2016. Spatial autocorrelation was tested using Moran's Index, which determines and measures the degree of clustering and dispersion of HCV infection in a country. RESULTS A total 114,928 HCV infection cases during a ten-year period with accurate geographic information were studied. Ages ranged between 16 and 50 years and the male to female ratio was 2:1. HCV infection was unevenly distributed in Libya, and its incidence increased steadily over the study period. Several hot spots and cold spots were found mainly in the southern and eastern regions of the country. CONCLUSION HCV infection in Libya was geographically variable, with several hot spots particularly in eastern and southern Libya associated with different demographic determinants. Future intervention planning should consider the geospatial variability and risk factors involved.
Collapse
Affiliation(s)
- Mohamed A. Daw
- Department of Medical Microbiology &Immunology, Faculty of Medicine, University of Tripoli, CC 82668 Tripoli, Libya
| | - Lutfi A. Buktir Ali
- Department of Infectious Disease, Tripoli Medical Centre, Tripoli, CC 82668 Tripoli, Libya
| | - Amina M. Daw
- Department of General Medicine, Faculty of Medicine, University of Tripoli, CC 82668 Tripoli, Libya
| | - Nadia E. M. Sifennasr
- Department of Medical Microbiology &Immunology, Faculty of Medicine, University of Tripoli, CC 82668 Tripoli, Libya
| | - Aghnyia A. Dau
- Department of Surgery, Tripoli Medical Centre, Faculty of Medicine, University of Tripoli, CC 82668 Tripoli, Libya
| | - Mohamed M. Agnan
- Department of Toxicology, Faculty of Medical Technology, AlgabalAl-garbi University, Nalut, Libya
| | - Abdallah El-Bouzedi
- Department of Laboratory Medicine, Faculty of Biotechnology, Tripoli University, CC 82668 Tripoli, Libya
| | - In association with the Libyan Study Group of Hepatitis & HIV
- Department of Medical Microbiology &Immunology, Faculty of Medicine, University of Tripoli, CC 82668 Tripoli, Libya
- Department of Infectious Disease, Tripoli Medical Centre, Tripoli, CC 82668 Tripoli, Libya
- Department of General Medicine, Faculty of Medicine, University of Tripoli, CC 82668 Tripoli, Libya
- Department of Surgery, Tripoli Medical Centre, Faculty of Medicine, University of Tripoli, CC 82668 Tripoli, Libya
- Department of Toxicology, Faculty of Medical Technology, AlgabalAl-garbi University, Nalut, Libya
- Department of Laboratory Medicine, Faculty of Biotechnology, Tripoli University, CC 82668 Tripoli, Libya
| |
Collapse
|
22
|
Cruz-Santos MD, Gomes-Gouvêa MS, Costa-Nunes JD, Malta-Romano C, Teles-Sousa M, Fonseca-Barros LM, Carrilho FJ, Paiva-Ferreira ADS, Rebello-Pinho JR. High Prevalence of Hepatitis B Subgenotype D4 in Northeast Brazil: an Ancient Relic from African Continent? Ann Hepatol 2018; 17:54-63. [PMID: 29311410 DOI: 10.5604/01.3001.0010.7535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Hepatitis B virus (HBV) infection leads to a chronic liver disease that is distributed worldwide. The characterization of HBV into genotypes/subgenotypes is not only a mere procedure for distinguishing different HBV strains around the world because determining their geographic distribution is crucial to understanding their spread across the world. MATERIAL AND METHODS We characterized different HBV genotypes and subgenotypes in five municipalities located in northeastern Maranhão, in the Brazilian north Atlantic coast. 92 HBsAg-positive individuals were submitted to PCR (polymerase chain reaction). Fifty samples were sequenced using automated Sanger sequencing and classified by phylogenetic methods. RESULTS Subgenotypes D4 and A1 were found in 42 (84%) and eight (16%) samples, respectively. To our knowledge, this is the first study to describe a high frequency of subgenotype D4 in any population. Subgenotype A1 is frequently found across Brazil, but D4 has been rarely detected and only in a few Brazilian states. This study shows the characterization of HBV subgenotypes from a population based study in the state of Maranhão, particularly in populations that do not have frequent contact with populations from other regions of the world. CONCLUSION Our findings showed a HBV subgenotype profile that probably reflect the viruses that were brought with the slave trade from Africa to Maranhão. This study also reinforces the need to evaluate the status of HBV dispersion not only in large urban centers, but also in the hinterland, to enable the implementation of effective control and treatment measures.
Collapse
Affiliation(s)
- Max D Cruz-Santos
- Laboratory of Tropical Gastroenterology and Hepatology, Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Michele S Gomes-Gouvêa
- Laboratory of Tropical Gastroenterology and Hepatology, Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Jomar D Costa-Nunes
- Center of Clinical Research, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Camila Malta-Romano
- Laboratory of Virology, LIM-52, São Paulo Institute of Tropical Medicine and Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Marinilde Teles-Sousa
- Center of Clinical Research, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Lena M Fonseca-Barros
- Center of Clinical Research, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Flair J Carrilho
- Laboratory of Tropical Gastroenterology and Hepatology, Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | | | - João R Rebello-Pinho
- Laboratory of Tropical Gastroenterology and Hepatology, Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, Brazil
| |
Collapse
|
23
|
Kostaki EG, Karamitros T, Stefanou G, Mamais I, Angelis K, Hatzakis A, Kramvis A, Paraskevis D. Unravelling the history of hepatitis B virus genotypes A and D infection using a full-genome phylogenetic and phylogeographic approach. eLife 2018; 7:36709. [PMID: 30082021 PMCID: PMC6118819 DOI: 10.7554/elife.36709] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/28/2018] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B virus (HBV) infection constitutes a global public health problem. In order to establish how HBV was disseminated across different geographic regions, we estimated the levels of regional clustering for genotypes D and A. We used 916 HBV-D and 493 HBV-A full-length sequences to reconstruct their global phylogeny. Phylogeographic analysis was conducted by the reconstruction of ancestral states using the criterion of parsimony. The putative origin of genotype D was in North Africa/Middle East. HBV-D sequences form low levels of regional clustering for the Middle East and Southern Europe. In contrast, HBV-A sequences form two major clusters, the first including sequences mostly from sub-Saharan Africa, and the second including sequences mostly from Western and Central Europe. Conclusion: We observed considerable differences in the global dissemination patterns of HBV-D and HBV-A and different levels of monophyletic clustering in relation to the regions of prevalence of each genotype.
Collapse
Affiliation(s)
- Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| | - Timokratis Karamitros
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
| | - Garyfallia Stefanou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| | - Ioannis Mamais
- Department of Health Sciences, School of SciencesEuropean University of CyprusNicosiaCyprus
| | - Konstantinos Angelis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, Faculty of Health ScienceUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| |
Collapse
|
24
|
Lai A, Sagnelli C, Presti AL, Cella E, Angeletti S, Spoto S, Costantino S, Sagnelli E, Ciccozzi M. What is changed in HBV molecular epidemiology in Italy? J Med Virol 2018; 90:786-795. [PMID: 29315661 DOI: 10.1002/jmv.25027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/25/2017] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) infection represents the most common cause of chronic liver diseases worldwide. Consequently, to the introduction of the universal HBV vaccination program, the prevalence of hepatitis B surface antigen was markedly reduced and less than 1% of the population of Western Europe and North America is chronically infected. To date, despite great advances in therapeutics, HBV chronic infection is considered an incurable disease. Ten hepatitis B virus genotypes (A-J) and several subgenotypes have been identified so far, based on intergroup divergences of 8% and 4%, respectively, in the complete viral genome. HBV-D genotype has been found throughout the world, with highest prevalence in the Mediterranean area. In the present review, several articles concerning HBV epidemiology, and phylogeny in Italy have been analyzed, mainly focusing on the changes occurred in the last decade.
Collapse
Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Alessandra L Presti
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM), National Institute of Health, Rome, Italy
| | - Eleonora Cella
- Unit of Clinical Laboratory Science, University of Campus Bio-Medico of Rome, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University of Campus Bio-Medico of Rome, Rome, Italy
| | - Silvia Spoto
- Internal Medicine Department, University Campus Bio-Medico of Rome, Rome, Italy
| | | | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Massimo Ciccozzi
- Unit of Clinical Laboratory Science, University of Campus Bio-Medico of Rome, Rome, Italy
| |
Collapse
|
25
|
Cella E, Golkocheva-Markova EN, Trandeva-Bankova D, Gregori G, Bruni R, Taffon S, Equestre M, Costantino A, Spoto S, Curtis M, Ciccaglione AR, Ciccozzi M, Angeletti S. The genetic diversity of hepatitis A genotype I in Bulgaria. Medicine (Baltimore) 2018; 97:e9632. [PMID: 29504993 PMCID: PMC5779762 DOI: 10.1097/md.0000000000009632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The purpose of this study was to analyze sequences of hepatitis A virus (HAV) Ia and Ib genotypes from Bulgarian patients to investigate the molecular epidemiology of HAV genotype I during the years 2012 to 2014. Around 105 serum samples were collected by the Department of Virology of the National Center of Infectious and Parasitic Diseases in Bulgaria. The sequenced region encompassed the VP1/2A region of HAV genome. The sequences obtained from the samples were 103. For the phylogenetic analyses, 5 datasets were built to investigate the viral gene in/out flow among distinct HAV subpopulations in different geographic areas and to build a Bayesian dated tree, Bayesian phylogenetic and migration pattern analyses were performed. HAV Ib Bulgarian sequences mostly grouped into a single clade. This indicates that the Bulgarian epidemic is partially compartmentalized. It originated from a limited number of viruses and then spread through fecal-oral local transmission. HAV Ia Bulgarian sequences were intermixed with European sequences, suggesting that an Ia epidemic is not restricted to Bulgaria but can affect other European countries. The time-scaled phylogeny reconstruction showed the root of the tree dating in 2008 for genotype Ib and in 1999 for genotype Ia with a second epidemic entrance in 2003. The Bayesian skyline plot for genotype Ib showed a slow but continuous growth, sustained by fecal-oral route transmission. For genotype Ia, there was an exponential growth followed by a plateau, which suggests better infection control. Bidirectional viral flow for Ib genotype, involving different Bulgarian areas, was observed, whereas a unidirectional flow from Sofia to Ihtiman for genotype Ia was highlighted, suggesting the fecal-oral transmission route for Ia.
Collapse
Affiliation(s)
- Eleonora Cella
- Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Elitsa N. Golkocheva-Markova
- NRL of Viral hepatitis, Virology department, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - Diljana Trandeva-Bankova
- NRL of Viral hepatitis, Virology department, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - Giulia Gregori
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome
| | - Roberto Bruni
- Viral Hepatitis Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases
| | - Stefania Taffon
- Viral Hepatitis Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases
| | - Michele Equestre
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità
| | - Angela Costantino
- Viral Hepatitis Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases
| | - Silvia Spoto
- Internal Medicine Department, University Hospital Campus Bio-Medico, Rome, Italy
| | - Melissa Curtis
- Department of Health, Human Performance and Recreation, Baylor University, Waco, TX, USA
| | - Anna Rita Ciccaglione
- Viral Hepatitis Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases
| | - Massimo Ciccozzi
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome
| |
Collapse
|
26
|
Forbi JC, Dillon M, Purdy MA, Drammeh BS, Tejada-Strop A, McGovern D, Xia GL, Lin Y, Ganova-Raeva LM, Campo DS, Thai H, Vaughan G, Haule D, Kutaga RP, Basavaraju SV, Kamili S, Khudyakov YE. Molecular epidemiology of hepatitis B virus infection in Tanzania. J Gen Virol 2017; 98:1048-1057. [PMID: 28537543 DOI: 10.1099/jgv.0.000776] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Despite the significant public health problems associated with hepatitis B virus (HBV) in sub-Saharan Africa, many countries in this region do not have systematic HBV surveillance or genetic information on HBV circulating locally. Here, we report on the genetic characterization of 772 HBV strains from Tanzania. Phylogenetic analysis of the S-gene sequences showed prevalence of HBV genotype A (HBV/A, n=671, 86.9 %), followed by genotypes D (HBV/D, n=95, 12.3 %) and E (HBV/E, n=6, 0.8 %). All HBV/A sequences were further classified into subtype A1, while the HBV/D sequences were assigned to a new cluster. Among the Tanzanian sequences, 84 % of HBV/A1 and 94 % of HBV/D were unique. The Tanzanian and global HBV/A1 sequences were compared and were completely intermixed in the phylogenetic tree, with the Tanzanian sequences frequently generating long terminal branches, indicating a long history of HBV/A1 infections in the country. The time to the most recent common ancestor was estimated to be 188 years ago [95 % highest posterior density (HPD): 132 to 265 years] for HBV/A1 and 127 years ago (95 % HPD: 79 to 192 years) for HBV/D. The Bayesian skyline plot showed that the number of transmissions 'exploded' exponentially between 1960-1970 for HBV/A1 and 1970-1990 for HBV/D, with the effective population of HBV/A1 having expanded twice as much as that of HBV/D. The data suggest that Tanzania is at least a part of the geographic origin of the HBV/A1 subtype. A recent increase in the transmission rate and significant HBV genetic diversity should be taken into consideration when devising public health interventions to control HBV infections in Tanzania.
Collapse
Affiliation(s)
- Joseph C Forbi
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Michael Dillon
- CDC Tanzania, Division of Global HIV/AIDS, Center for Global Health, Centers for Disease Control and Prevention, Dar es Salaam, Tanzania
| | - Michael A Purdy
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Bakary S Drammeh
- HIV Prevention Branch, Division of Global HIV/AIDS, Center for Global Health, CDC, Dar es Salaam, Tanzania
| | - Alexandra Tejada-Strop
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Daniel McGovern
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Guo-Liang Xia
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Yulin Lin
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Lilia M Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - David S Campo
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Hong Thai
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Gilberto Vaughan
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Dunstan Haule
- Tanzania National Blood Transfusion Services, Ministry of Health and Social Welfare, Dar es Salaam, Tanzania
| | - Regina P Kutaga
- US Centers for Disease Control and Prevention, Dar es Salaam, Tanzania
| | - Sridhar V Basavaraju
- HIV Prevention Branch, Division of Global HIV/AIDS, Center for Global Health, CDC, Dar es Salaam, Tanzania
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| | - Yury E Khudyakov
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, Georgia, USA
| |
Collapse
|
27
|
Ciccozzi M, Chaouch H, Lo Presti A, Taffon S, Villano U, Equestre M, Bruni R, Marcantonio C, Tritarelli E, Cella E, Blasi A, Aouni M, Letaief A, Ciccaglione AR. Evolutionary dynamics of HBV-D7 subgenotype in Tunisia. J Med Virol 2016; 89:469-475. [PMID: 27543368 DOI: 10.1002/jmv.24665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2016] [Indexed: 12/11/2022]
Abstract
Hepatitis B virus (HBV) is the main cause of diseases liver related infecting more than 200 milion persons worldwide. HBV infection shows high level of prevalence in South-East Europe and in Mediterranean basin. In Tunisia, a country with an intermediate level endemicity, HbsAg prevalence ranges from 2 to 5%. Most of the HBV isolates from Tunisia were classified as subgenotype D7 whose circulation is restricted to a specific area of North Africa including Maghreb region. In this paper, the phylogeny of HBV-D7 isolated from 38 Tunisian patients was investigated by analyzing the S gene region of HBV. A Bayesian coalescent-based framework was used to estimate the origin of the HBV-D7 in the country. The Tunisian D7 isolates were found to share a common ancestor whose origin was traced back to 1958. Population dynamics indicated that HBV-D7 epidemic in Tunisia grew exponentially from 1960s to 1990s. After that, the curve reached a plateau around the years 2000 likely due to the implementation of the infant vaccination program in 1996. Epidemiological data suggested that the exponential growth phase was likely sustained by intra-familial transmission events occurring during infancy. Further characterization of HBV-D7 isolates should be performed to evaluate, in the post-vaccination era, the emergence of new transmission routes, and to monitor the efficacy of the vaccination program. J. Med. Virol. 89:469-475, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,University Hospital Campus Bio-Medico, Rome, Italy
| | - Houda Chaouch
- Department of Infectious Diseases, Viral Hepatitis Research Unit (UR12SP35), University Hospital Farhat Hached, Sousse, Tunisia.,Faculty of Pharmacy, Laboratory of Infectious Diseases and Biological Agents, University of Monastir, Monastir, Tunisia
| | - Alessandra Lo Presti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Stefania Taffon
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Umbertina Villano
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Michele Equestre
- Department of Cell Biology and Neurosciences, Clinical Diagnostics and Therapy of Degenerative Diseases of the Central Nervous System Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Bruni
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Cinzia Marcantonio
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Elena Tritarelli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Eleonora Cella
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Aletheia Blasi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,University Hospital Campus Bio-Medico, Rome, Italy
| | - Mahjoub Aouni
- Faculty of Pharmacy, Laboratory of Infectious Diseases and Biological Agents, University of Monastir, Monastir, Tunisia
| | - Amel Letaief
- Department of Infectious Diseases, Viral Hepatitis Research Unit (UR12SP35), University Hospital Farhat Hached, Sousse, Tunisia
| | - Anna Rita Ciccaglione
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Rome, Italy
| |
Collapse
|
28
|
Analysis of the Molecular Evolution of Hepatitis B Virus Genotypes in Symptomatic Acute Infections in Argentina. PLoS One 2016; 11:e0159509. [PMID: 27433800 PMCID: PMC4951016 DOI: 10.1371/journal.pone.0159509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 07/05/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) is a globally distributed human pathogen that leads to both self-limited and chronic infections. At least eight genotypes (A-H) with distinct geographical allocations and phylodynamic behaviors have been described. They differ substantially in many virological and probably some clinical parameters. The aim of this study was to analyze full-length HBV genome sequences from individuals with symptomatic acute HBV infections using phylogenetic and coalescent methods. The phylogenetic analysis resulted in the following subgenotype distribution: F1b (52.7%), A2 (18.2%), F4 (18.2%) and A1, B2, D3 and F2a 1.8% each. These results contrast with those previously reported from chronic infections, where subgenotypes F1b, F4, A2 and genotype D were evenly distributed. This differential distribution might be related to recent internal migrations and/or intrinsic biological features of each viral genotype that could impact on the probability of transmission. The coalescence analysis showed that after a diversification process started in the 80s, the current sequences of subgenotype F1b were grouped in at least four highly supported lineages, whereas subgenotype F4 revealed a more limited diversification pattern with most lineages without offspring in the present. In addition, the genetic characterization of the studied sequences showed that only two of them presented mutations of clinical relevance at S codifyng region and none at the polymerase catalytic domains. Finally, since the acute infections could be an expression of the genotypes currently being transmitted to new hosts, the predominance of subgenotype F1b might have epidemiological, as well as, clinical relevance due to its potential adverse disease outcome among the chronic cases.
Collapse
|
29
|
Abu Zeid WM, Ramadan DI, Shemis MA. Prevalence of mutations within major hydrophilic region of hepatitis B virus and their correlation with genotypes among chronically infected patients in Egypt. Arab J Gastroenterol 2016; 17:34-40. [PMID: 27055927 DOI: 10.1016/j.ajg.2016.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/03/2016] [Accepted: 03/08/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND STUDY AIMS Mutations within the major hydrophilic region (MHR) of the hepatitis B surface antigen (HBsAg) have been reported in relation to viral persistence by evasion from vaccine and immunotherapy, severity of liver disease and lack of detection by commercial kits. The aim of this study was to elucidate the circulation of hepatitis B virus (HBV) genotypes, subgenotypes and serotypes in Egypt, with recognition of the pattern and prevalence of MHR mutations possibly occurring during the course of the disease. PATIENTS AND METHODS Eighty-eight samples from patients with chronic HBV infection were included in the study. The surface protein-encoding gene (S gene) in the HBV genome was subjected to amplification and partial sequencing. RESULTS Based on phylogenetic analysis, only genotype D was found circulating among patients. The majority of isolates belonged to subgenotype D3 (86.3%), followed by D7 (8%), then D5 (3.4%) and lastly D1 (2.3%). Two subtypes were identified: ayw2 (97%) and ayw3 (2%). The 'w' sub-determinant was not defined in one isolate (1%). A significant proportion of patients (13/88, 14.8%) exhibited mutations in the MHR, 10 of whom harboured mutations in the 'a' determinant region and three outside. The first loop comprised four patients with three mutations (P127S, P127T and Y134F). The second loop contained six patients, all with one mutation, S143L, which was most frequently encountered in this study (6.8%). CONCLUSIONS We conclude that genotype D, subgenotype D3 and HBsAg subtype ayw2 are the most common types circulating in Egypt, which account for 100%, 86.3% and 97% of the population, respectively, with a moderate degree of MHR mutations.
Collapse
Affiliation(s)
| | - Dalia I Ramadan
- Department of Clinical and Chemical Pathology, Kasr Alainy School of Medicine, Cairo University, Cairo, Egypt.
| | - Mohamed A Shemis
- Department of Biochemistry & Molecular Biology, Theodor Bilharz Research Institute, Giza, Egypt
| |
Collapse
|
30
|
Zampino R, Boemio A, Sagnelli C, Alessio L, Adinolfi LE, Sagnelli E, Coppola N. Hepatitis B virus burden in developing countries. World J Gastroenterol 2015; 21:11941-11953. [PMID: 26576083 PMCID: PMC4641116 DOI: 10.3748/wjg.v21.i42.11941] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 07/23/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infection has shown an intermediate or high endemicity level in low-income countries over the last five decades. In recent years, however, the incidence of acute hepatitis B and the prevalence of hepatitis B surface antigen chronic carriers have decreased in several countries because of the HBV universal vaccination programs started in the nineties. Some countries, however, are still unable to implement these programs, particularly in their hyperendemic rural areas. The diffusion of HBV infection is still wide in several low-income countries where the prevention, management and treatment of HBV infection are a heavy burden for the governments and healthcare authorities. Of note, the information on the HBV epidemiology is scanty in numerous eastern European and Latin-American countries. The studies on molecular epidemiology performed in some countries provide an important contribution for a more comprehensive knowledge of HBV epidemiology, and phylogenetic studies provide information on the impact of recent and older migratory flows.
Collapse
|
31
|
Hirzel C, Wandeler G, Owczarek M, Gorgievski-Hrisoho M, Dufour JF, Semmo N, Zürcher S. Molecular epidemiology of hepatitis B virus infection in Switzerland: a retrospective cohort study. BMC Infect Dis 2015; 15:483. [PMID: 26518625 PMCID: PMC4628344 DOI: 10.1186/s12879-015-1234-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 10/19/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chronic hepatitis B virus (HBV) infection affects up to 7% of the European population. Specific HBV genotypes are associated with rapid progression to end-stage liver disease and sub-optimal interferon treatment responses. Although the geographic distribution of HBV genotypes differs between regions, it has not been studied in Switzerland, which lies at the crossroads of Europe. METHODS In a retrospective analysis of 465 HBV samples collected between 2002 and 2013, we evaluated the HBV genotype distribution and phylogenetic determinants, as well as the prevalence of serological evidence of hepatitis delta, hepatitis C and HIV infections in Switzerland. Baseline characteristics of patients were compared across their region of origin using Fisher's exact test and ANOVA, and risk factors for HBeAg positivity were assessed using logistic regression. RESULTS The Swiss native population represented 15.7% of HBV-infected patients living in Switzerland. In the overall population, genotype D was most prevalent (58.3%), whereas genotype A (58.9%) was the predominant genotype among the Swiss native population. The prevalence of patients with anti-HDV antibodies was 4.4%. Patients of Swiss origin were most likely to be HBeAg-positive (38.1%). HBV genotypes of patients living in Switzerland but sharing the same original region of origin were consistent with their place of birth. CONCLUSIONS The molecular epidemiology of HBV infection in Switzerland is driven by migration patterns and not by the genotype distribution of the native population. The prevalence of positive anti-HDV antibodies in our cohort was very low.
Collapse
Affiliation(s)
- Cédric Hirzel
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.
| | - Gilles Wandeler
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.
| | - Marta Owczarek
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
| | | | - Jean-Francois Dufour
- Hepatology Unit, Department of Visceral Surgery and Medicine University Hospital Bern, Bern, Switzerland.
| | - Nasser Semmo
- Hepatology Unit, Department of Visceral Surgery and Medicine University Hospital Bern, Bern, Switzerland.
| | - Samuel Zürcher
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
| |
Collapse
|
32
|
Moussa S, Brah S, Parola P, Gerolami R, Gamerre M, Boubli L, Ruiz JM, Ravaux I, Mokhtari S, Mancini J, Romera MH, Motte A, Tamalet C, Colson P. Epidemiological, clinical, virological features of hepatitis B newly diagnosed in 2011 in Marseille University hospitals, southeastern France. J Med Virol 2015; 88:828-36. [PMID: 26439319 DOI: 10.1002/jmv.24398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) infection is a public health problem. In France, 0.68% of adults are chronically infected. We aimed to describe the epidemiological, virological and clinical characteristics of HBV infections newly diagnosed in 2011 in University hospitals of Marseille, the second largest French city. HBV serology was performed for 18,130 sera from 15,744 patients. A total of 167 patients were newly-diagnosed with HBV based upon the detection of hepatitis B surface antigen and anti-hepatitis B core antibodies. Clinico-epidemiological features were analyzed for 78 patients. Patients included a majority of men (59%), women being significantly younger with a mean age of 36 ± 17 versus 43.5 ± 16.2 years (P = 0.009). Country of birth was available for 52 patients and 35% of them originated from sub-Saharan Africa. Levels of the liver biological parameters were significantly lower in women compared to men, in whom mean alanine aminotransferase and gammaglutamyl transferase levels were 24 ± 39 versus 37 ± 36 IU/l (P = 0.0001) and 20 ± 20 versus 51 ± 53 IU/l (P = 0.0001), respectively. Co-infections with hepatitis C and human immunodeficiency viruses were found in 5% and 6% of the patients, respectively. HBV DNA was detectable in 90% of the HBeAg-negative patients. In addition, there was a positive correlation between the HBsAg titer and the HBV DNA level (P = 0.001). Genotype D was the most common HBV genotype and was found in 53% of the patients tested, followed by genotype E (21%). HBV remains a major concern with a slightly greater number of new diagnoses than in 2004. HBV genetic diversity was substantial in the present cohort.
Collapse
Affiliation(s)
- Sahada Moussa
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Souleymane Brah
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France.,Aix-Marseille University, URMITE UM63 CNRS 7278 IRD 198 INSERM U1905, Marseille, France
| | - Philippe Parola
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France.,Aix-Marseille University, URMITE UM63 CNRS 7278 IRD 198 INSERM U1905, Marseille, France
| | - René Gerolami
- Service d'Hépato-Gastro-Entérologie, Centre Hospitalo-Universitaire Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Marc Gamerre
- Service d'Hépato-Gastro-Entérologie, Centre Hospitalo-Universitaire Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Léon Boubli
- Service de Gynecologie-Obstrétique, Centre Hospitalo-Universitaire Nord, Assistance Publique-Hôpitaux de Marseille, chemin des Bourrely, Marseille, France
| | - Jean-Marie Ruiz
- Assistance-Publique Hôpitaux de Marseille, Hôpitaux Sud, Service de Médecine en milieu pénitentiaire, Centre pénitentiaire de Marseille, Marseille, France
| | - Isabelle Ravaux
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Saada Mokhtari
- Aix-Marseille University, URMITE UM63 CNRS 7278 IRD 198 INSERM U1905, Marseille, France
| | - Julien Mancini
- Assistance Publique-Hôpitaux de Marseille, hôpital Timone, Service Biostatistique et Technologies de l'Information et de la Communication, Marseille, France
| | - Marie-Hélène Romera
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Anne Motte
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Catherine Tamalet
- Aix-Marseille University, URMITE UM63 CNRS 7278 IRD 198 INSERM U1905, Marseille, France.,IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Colson
- Aix-Marseille University, URMITE UM63 CNRS 7278 IRD 198 INSERM U1905, Marseille, France.,IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| |
Collapse
|
33
|
Vratnica Z, Zehender G, Ebranati E, Sorrentino C, Lai A, Vujošević D, Veo C, Lo Presti A, Cella E, Giovanetti M, Laušević D, Galli M, Ciccozzi M, Mugoša B. Hepatitis B virus genotype and subgenotype prevalence and distribution in Montenegro. J Med Virol 2015; 87:807-13. [PMID: 25712706 DOI: 10.1002/jmv.24083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2014] [Indexed: 12/25/2022]
Abstract
The Mediterranean area and the Balkans in particular show the highest level of genetic heterogeneity of HBV in Europe. Data about the circulation of HBV genotypes in Montenegro are lacking. It was studied the prevalence and distribution of HBV genot/subgenotypes in a total of 150 HBV infected patients living in Montenegro. Phylogenetic analysis of 136 successfully amplified P sequences showed a high degree of genetic heterogeneity of HBV in Montenegro. Subgenotype D2 (36.8%) and D3 (32.3%) were the most prevalent, followed by genotype A (subgenotype A2 in all of the cases-19.8%). Eight patients were infected with recombinant strains. HBV-D1 which is the most spread HBV subgenotype in the south-eastern Mediterranean countries, seems to be relatively rare in Montenegro, suggesting a penetration of HBV more probably from North-East or West than from Eastern Mediterranean countries. The relatively different prevalence of D3 and A2 among subjects infected through sexual route, seems to confirm the association of these subgenotypes with different route of transmissions (mainly parenteral for D3 and mainly sexual for A2) even in Montenegro. The low prevalence of D2 among children and its absence in perinatal transmission, suggests that this subgenotype circulated prevalently in the past. If this is due to changes in the most prevalent way of transmission and in the recent different contacts of Montenegro with other European countries, it remains to be established by other larger studies.
Collapse
|
34
|
Pineda-Peña AC, Faria NR, Mina T, Amini-Bavil-Olyaee S, Alavian SM, Lemey P, Maes P, Van Ranst M, Pourkarim MR. Epidemiological history and genomic characterization of non-D1 HBV strains identified in Iran. J Clin Virol 2014; 63:38-41. [PMID: 25600602 DOI: 10.1016/j.jcv.2014.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/11/2014] [Accepted: 12/13/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) has been classified into eight genotypes and forty subgenotypes. Genotype D of HBV is the most worldwide distributed genotype and HBV subgenotype D1 has been isolated from Iranian patients. OBJECTIVE To characterize for the first time complete genomes of recently emerged non-D1 strains in Iran. STUDY DESIGN HBV complete genomes isolated from 9 Iranian HBV carriers were sequenced. Different diversities of the ORFs were mapped and evolutionary history relationships were investigated. RESULTS Phylogenetic analysis identified four D2 subgenotypes and five D3 subgenotypes of HBV in the studied patients. Of note, D2 strains clustered with strains from Lebanon and Syria. The time of the most recent common ancestor (TMRCA) of the first cluster of D2 was dated at 1953 (BCI=1926, 1976) while the second cluster was dated at 1947 (BCI=1911, 1978). All five Iranian D3 strains formed a monophyletic cluster with Indian strain and dated back to 1967 (BCI=1946, 1987). Surprisingly, two D3 strains had an adw2 subtype. Interestingly, more than 80% of the present strains showed precore mutations, while two isolates carried basal core promoter variation. CONCLUSION Iranian D2 and D3 isolates were introduced on at least two and one occasion in Iran and diverged from west and south Asian HBV strains, respectively. Considering the impact of the different (sub) genotypes on clinical outcome, exploring the distinct mutational patterns of Iranian D1 and non-D1 strains is of clinical importance.
Collapse
Affiliation(s)
- Andrea-Clemencia Pineda-Peña
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium; Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia; Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia; Centro de Malária e Outras Doenc¸ as Tropicais and Unidade de Saúde Pública Internacional e Bioestatística, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, South Parks Road, OX1-3PS, Oxford, United Kingdom
| | - Thomas Mina
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Samad Amini-Bavil-Olyaee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Harlyne J. Norris Cancer Research Tower, Los Angeles, CA 90033, USA
| | - Seyed Moayed Alavian
- Middle East Liver Disease Clinics, Sepahbod Gharani Ave, 14155-3651 Tehran, Iran
| | - Philippe Lemey
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Piet Maes
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium; Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Hemmat Exp. Way, 14665-1157, Tehran, Iran.
| |
Collapse
|
35
|
Bokharaei-Salim F, Keyvani H, Monavari SH, Esghaei M, Fakhim S, Ataei Pirkooh A, Behnava B. Distribution of hepatitis B virus genotypes in azerbaijani patients with chronic hepatitis B infection. HEPATITIS MONTHLY 2014; 14:e25105. [PMID: 25685166 PMCID: PMC4310019 DOI: 10.5812/hepatmon.25105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 11/18/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis B virus (HBV) has been classified into ten genotypes (A-J) based on genome sequence divergence, which is very important for etiological and clinical investigations. HBV genotypes have distinct geographical distributions worldwide. OBJECTIVES The aim of this study was to investigate the distribution of HBV genotypes among Azerbaijani patients with chronic hepatitis B, came from the Republic of Azerbaijan country to Iran to receive medical care. PATIENTS AND METHODS One hundred and three patients with chronic HBV infection, referred to hospitals related to Iran University of Medical Sciences and Tehran Hepatitis Center from August 2011 to July 2014, were enrolled in this cross sectional study. About 3-milliliter of peripheral blood was taken from each patient. After viral DNA extraction, HBV genotypes were tested using the INNO-LiPA™ HBV kit (Innogenetics, Ghent, Belgium). HBV genotyping was confirmed using sequencing of hepatitis B surface antigen (HBsAg) and polymerase (pol) regions of HBV. RESULTS The mean age of patients was 35.9 ± 11.7 years (19-66). Of 103 patients, 72 (69.9%) were male. In the present study, the predominant HBV genotype was D (93.2%) followed by genotype A (5.8%) and concurrent infection with A and D genotypes (0.97%). CONCLUSIONS The main and frequent HBV genotype among Azerbaijani patients with chronic hepatitis B virus infection was genotype D followed by genotype A.
Collapse
Affiliation(s)
- Farah Bokharaei-Salim
- Department of Virology, Iran University of Medical Sciences, Tehran, IR Iran
- Corresponding Author: Farah Bokharaei Salim, Department of Virology, Iran University of Medical Sciences, Tehran, IR Iran. Tel/Fax: +98-2188602205, E-mail:
| | - Hossein Keyvani
- Department of Virology, Iran University of Medical Sciences, Tehran, IR Iran
| | | | - Maryam Esghaei
- Department of Virology, Iran University of Medical Sciences, Tehran, IR Iran
| | - Shahin Fakhim
- Department of Civil Engineering, Faculty of Engineering, Payame Noor University, Karaj, IR Iran
| | | | - Bita Behnava
- Middle East Liver Diseases Center, Tehran, IR Iran
- Iran Hepatitis Network, Tehran, IR Iran
| |
Collapse
|
36
|
Banerjee P, Mondal RK, Nandi M, Ghosh S, Khatun M, Chakraborty N, Bhattacharya S, RoyChoudhury A, Banerjee S, Santra A, Sil S, Chowdhury A, Bhaumik P, Datta S. A rare HBV subgenotype D4 with unique genomic signatures identified in north-eastern India--an emerging clinical challenge? PLoS One 2014. [PMID: 25295865 DOI: 10.1371/journal.pone.0109425.ecollection] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND/AIMS HBV has been classified into ten genotypes (A-J) and multiple subgenotypes, some of which strongly influence disease outcome and their distribution also correlate with human migration. HBV infection is highly prevalent in India and its diverse population provides an excellent opportunity to study the distinctiveness of HBV, its evolution and disease biology in variegated ethnic groups. The North-East India, having international frontiers on three sides, is one of the most ethnically and linguistically diverse region of the country. Given the paucity of information on molecular epidemiology of HBV in this region, the study aimed to carry out an in-depth genetic characterization of HBV prevailing in North-East state of Tripura. METHODS From sera of chronically HBV infected patients biochemical/serological tests, HBV DNA quantification, PCR-amplification, sequencing of PreS/S or full-length HBV genomes were done. HBV genotype/subgenotype determination and sequence variability were assessed by MEGA5-software. The evolutionary divergence times of different HBV subgenotypes were estimated by DNAMLK/PHYLIP program while jpHMM method was used to detect any recombination event in HBV genomes. RESULTS HBV genotypes D (89.5%), C (6.6%) and A (3.9%) were detected among chronic carriers. While all HBV/A and HBV/C isolates belonged to subgenotype-A1 and C1 respectively, five subgenotypes of HBV/D (D1-D5) were identified including the first detection of rare D4. These non-recombinant Indian D4 (IndD4) formed a distinct phylogenetic clade, had 2.7% nucleotide divergence and recent evolutionary radiation than other global D4. Ten unique amino acids and 9 novel nucleotide substitutions were identified as IndD4 signatures. All IndD4 carried T120 and R129 in ORF-S that may cause immune/vaccine/diagnostic escape and N128 in ORF-P, implicated as compensatory Lamivudine resistance mutation. CONCLUSIONS IndD4 has potential to undermine vaccination programs or anti-viral therapy and its introduction to North-East India is believed to be linked with the settlement of ancient Tibeto-Burman migrants from East-Asia.
Collapse
Affiliation(s)
- Priyanka Banerjee
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Rajiv Kumar Mondal
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Madhuparna Nandi
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Sumantra Ghosh
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Mousumi Khatun
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | | | | | | | - Soma Banerjee
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Amal Santra
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | | | - Abhijit Chowdhury
- Department of Hepatology, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | | | - Simanti Datta
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| |
Collapse
|
37
|
Banerjee P, Mondal RK, Nandi M, Ghosh S, Khatun M, Chakraborty N, Bhattacharya S, RoyChoudhury A, Banerjee S, Santra A, Sil S, Chowdhury A, Bhaumik P, Datta S. A rare HBV subgenotype D4 with unique genomic signatures identified in north-eastern India--an emerging clinical challenge? PLoS One 2014; 9:e109425. [PMID: 25295865 PMCID: PMC4190083 DOI: 10.1371/journal.pone.0109425] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 08/31/2014] [Indexed: 01/01/2023] Open
Abstract
Background/Aims HBV has been classified into ten genotypes (A–J) and multiple subgenotypes, some of which strongly influence disease outcome and their distribution also correlate with human migration. HBV infection is highly prevalent in India and its diverse population provides an excellent opportunity to study the distinctiveness of HBV, its evolution and disease biology in variegated ethnic groups. The North-East India, having international frontiers on three sides, is one of the most ethnically and linguistically diverse region of the country. Given the paucity of information on molecular epidemiology of HBV in this region, the study aimed to carry out an in-depth genetic characterization of HBV prevailing in North-East state of Tripura. Methods From sera of chronically HBV infected patients biochemical/serological tests, HBV DNA quantification, PCR-amplification, sequencing of PreS/S or full-length HBV genomes were done. HBV genotype/subgenotype determination and sequence variability were assessed by MEGA5-software. The evolutionary divergence times of different HBV subgenotypes were estimated by DNAMLK/PHYLIP program while jpHMM method was used to detect any recombination event in HBV genomes. Results HBV genotypes D (89.5%), C (6.6%) and A (3.9%) were detected among chronic carriers. While all HBV/A and HBV/C isolates belonged to subgenotype-A1 and C1 respectively, five subgenotypes of HBV/D (D1–D5) were identified including the first detection of rare D4. These non-recombinant Indian D4 (IndD4) formed a distinct phylogenetic clade, had 2.7% nucleotide divergence and recent evolutionary radiation than other global D4. Ten unique amino acids and 9 novel nucleotide substitutions were identified as IndD4 signatures. All IndD4 carried T120 and R129 in ORF-S that may cause immune/vaccine/diagnostic escape and N128 in ORF-P, implicated as compensatory Lamivudine resistance mutation. Conclusions IndD4 has potential to undermine vaccination programs or anti-viral therapy and its introduction to North-East India is believed to be linked with the settlement of ancient Tibeto-Burman migrants from East-Asia.
Collapse
Affiliation(s)
- Priyanka Banerjee
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Rajiv Kumar Mondal
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Madhuparna Nandi
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Sumantra Ghosh
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Mousumi Khatun
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | | | | | | | - Soma Banerjee
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | - Amal Santra
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | | | - Abhijit Chowdhury
- Department of Hepatology, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
| | | | - Simanti Datta
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
- * E-mail:
| |
Collapse
|
38
|
Sagnelli C, Ciccozzi M, Pisaturo M, Zehender G, Lo Presti A, Alessio L, Starace M, Lovero D, Sagnelli E, Coppola N. Molecular epidemiology of hepatitis B virus genotypes circulating in acute hepatitis B patients in the Campania region. J Med Virol 2014; 86:1683-93. [PMID: 24980631 DOI: 10.1002/jmv.24005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2014] [Indexed: 12/11/2022]
Abstract
Fifty-three HBV-DNA-positive patients with symptomatic acute hepatitis B were enrolled from 1999 to 2010 to evaluate molecular and phylogenetic changes in HBV in southern Italy. HBV polymerase region was evaluated by direct sequencing in plasma samples obtained at first observation. Different data sets were aligned and a phylogenetic tree was inferred using PhyML program. Statistical robustness was confirmed with a bootstrap analysis. A Bayesian Markov chain Monte Carlo method and a Bayesian skyline plot were used to estimate the evolution of our samples. The dN/dS rate (ω) was estimated by the maximum likelihood approach to investigate the presence of codons under positive selection. The MacClade program was used to test viral gene out/in flow only among HBV-D3 subgenotype patients with different risk factors. Of the 53 patients, 83% were born in Italy and 17% were foreigners. HBV genotype D was prevalent (64.1%), followed by genotype A (26.4%), E (3.8%), and F (5.7%). The prevalent subgenotype was D3 (70.6%). The Bayesian tree of the 24 D3 subgenotypes showed two main clades both dated 1994; 40% of viral gene flow observed was from intravenous drugs users and heterosexual patients. Phylogenetic analysis of HBV isolates showed that HBV-D3 remains the prevalent genotype, but also subgenotype A2 has become frequent in southern Italy. This may be of clinical relevance in years to come, since patients with HBV-genotype-A chronic infection less frequently than those with genotype D develop HBeAg-negative chronic hepatitis and respond more frequently to alfa-interferon treatment.
Collapse
Affiliation(s)
- Caterina Sagnelli
- Department of Clinical and Experimental Medicine and Surgery "F. Magrassi e A. Lanzara", Second University of Naples, Naples, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Nyan DC, Ulitzky LE, Cehan N, Williamson P, Winkelman V, Rios M, Taylor DR. Rapid detection of hepatitis B virus in blood plasma by a specific and sensitive loop-mediated isothermal amplification assay. Clin Infect Dis 2014; 59:16-23. [PMID: 24704724 PMCID: PMC4305128 DOI: 10.1093/cid/ciu210] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 03/25/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) is an important blood-borne pathogen that causes hepatic inflammation and can lead to liver cirrhosis and hepatocellular carcinoma. Conventional methods of HBV detection are time consuming and require highly trained personnel and elaborate equipment. This report describes the development of a rapid, simple, specific, and sensitive loop-mediated isothermal amplification assay (LAMP) for detection of HBV genotypes A, B, C, D, E, and F in blood samples. METHODS HBV standard plasma panels and clinical donor plasma specimens were used for the development and validation of the LAMP assay. Amplification was performed at 60°C for 60 minutes using extracted DNA or heat-treated plasma specimens without DNA extraction. The assay was evaluated for its ability to detect various HBV genotypes and for its sensitivity, specificity, and time-point of detection. RESULTS The LAMP assay detected HBV genotypes A-F and demonstrated a sensitivity of 10-100 IU per reaction of HBV DNA. The assay also detected 69 of 75 (92%) HBV-positive donor plasma specimens tested and demonstrated a specificity of 100%. CONCLUSIONS These results demonstrate that our HBV-LAMP assay is rapid, sensitive and specific, and capable of detecting the major HBV genotypes. This assay could be used in clinical point-of-care settings, mainly in endemic and resource-limited environments for HBV diagnostics, donor screening, epidemiological studies, and therapeutic monitoring of patients undergoing antiviral treatment.
Collapse
Affiliation(s)
- Dougbeh-Chris Nyan
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| | - Laura E. Ulitzky
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| | - Nicoleta Cehan
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| | | | | | - Maria Rios
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| | - Deborah R. Taylor
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| |
Collapse
|
40
|
Zehender G, Ebranati E, Gabanelli E, Sorrentino C, Lo Presti A, Tanzi E, Ciccozzi M, Galli M. Enigmatic origin of hepatitis B virus: An ancient travelling companion or a recent encounter? World J Gastroenterol 2014; 20:7622-7634. [PMID: 24976700 PMCID: PMC4069291 DOI: 10.3748/wjg.v20.i24.7622] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/08/2014] [Accepted: 03/13/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is the leading cause of liver disease and infects an estimated 240 million people worldwide. It is characterised by a high degree of genetic heterogeneity because of the use of a reverse transcriptase during viral replication. The ten genotypes (A-J) that have been described so far further segregate into a number of subgenotypes which have distinct ethno-geographic distribution. Genotypes A and D are ubiquitous and the most prevalent genotypes in Europe (mainly represented by subgenotypes D1-3 and A2); genotypes B and C are restricted to eastern Asia and Oceania; genotype E to central and western Africa; and genotypes H and F (classified into 4 subgenotypes) to Latin America and Alaska. This review summarises the data obtained by studying the global phylodynamics and phylogeography of HBV genotypes, particularly those concerning the origin and dispersion histories of genotypes A, D, E and F and their subgenotypes. The lack of any consensus concerning the HBV substitution rate and the conflicting data obtained using different calibration approaches make the time of origin and divergence of the various genotypes and subgenotypes largely uncertain. It is hypothesised that HBV evolutionary rates are time dependent, and that the changes depend on the main transmission routes of the genotypes and the dynamics of the infected populations.
Collapse
|
41
|
Pourkarim MR, Amini-Bavil-Olyaee S, Kurbanov F, Van Ranst M, Tacke F. Molecular identification of hepatitis B virus genotypes/subgenotypes: revised classification hurdles and updated resolutions. World J Gastroenterol 2014; 20:7152-68. [PMID: 24966586 PMCID: PMC4064061 DOI: 10.3748/wjg.v20.i23.7152] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/28/2013] [Accepted: 01/02/2014] [Indexed: 02/06/2023] Open
Abstract
The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term "recombino-subgenotype". Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term "immigro-subgenotype" to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.
Collapse
|
42
|
Zehender G, Ebranati E, Lai A, Luzzago C, Paladini S, Tagliacarne C, Galli C, Galli M, Ciccozzi M, Zanetti AR, Romanò L. Phylogeography and phylodynamics of European genotype 3 hepatitis E virus. INFECTION GENETICS AND EVOLUTION 2014; 25:138-43. [PMID: 24787998 DOI: 10.1016/j.meegid.2014.04.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/18/2014] [Accepted: 04/20/2014] [Indexed: 01/22/2023]
Abstract
Hepatitis E virus is classified into four genotypes that have different geographical and host distributions. The main cause of sporadic autochthonous type E acute hepatitis in developed countries is genotype 3, which has a worldwide distribution and widely infects pigs. The aim of this study was to make hypotheses concerning the origin and global dispersion routes of this genotype by reconstructing the spatial and temporal dynamics of 208 HEV genotype 3 ORF-2 sequences (retrieved from public databases) isolated in different geographical areas. The evolutionary rates, time of the most recent common ancestors (tMRCAs), epidemic growth and phylogeography of HEV-3 were co-estimated using a MCMC Bayesian method. The maximum clade credibility tree showed the existence of two distinct main clades: clade A, which consists of only European subtypes (HEV-3e and 3f), and clade B, which consists of European subtype 3c and all of the Asian subtypes (3a, 3b and 3d) sharing a common ancestor, which most probably existed in Asia in 1920s. All of the North American isolates belonged to Asian subtype 3a. On the basis of our time-scaled phylogeographical reconstruction, we hypothesise that after originating in the early 1800s in Europe, HEV reached Asia in the first decades of 1900, and then moved to America probably in the 1970s-1980s. Analysis of the skyline plot showed a sharp increase of the number of infections between the 1980s and 2005, thus suggesting the intervention of new and highly efficient routes of transmission possibly related to changes in the pig industry.
Collapse
Affiliation(s)
- Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.
| | - Erika Ebranati
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Camilla Luzzago
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy
| | - Sara Paladini
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Catia Tagliacarne
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic, and Immunomediated Disease, National Institute of Health, Rome, Italy; University Biomedical Campus, Rome, Italy
| | | | - Luisa Romanò
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| |
Collapse
|
43
|
Saha D, Pal A, Biswas A, Panigrahi R, Sarkar N, Das D, Sarkar J, Guha SK, Saha B, Chakrabarti S, Chakravarty R. Molecular characterization of HBV strains circulating among the treatment-naive HIV/HBV co-infected patients of eastern India. PLoS One 2014; 9:e90432. [PMID: 24587360 PMCID: PMC3938687 DOI: 10.1371/journal.pone.0090432] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 01/29/2014] [Indexed: 02/07/2023] Open
Abstract
Previously we reported that the exposure to hepatitis B virus (HBV) infection serves as a major threat among the treatment naive HIV infected population of eastern India. Hence, molecular characterization of these strains is of utmost importance in order to identify clinically significant HBV mutations. A total of 85 treatment naive HIV/HBV co-infected participants were included of whom the complete basal core promoter/precore region, the core and the whole envelope gene could be successfully sequenced for 59, 57 and 39 isolates respectively. Following phylogenetic analysis, it was found that HBV/D was the predominant genotype with HBV/D2 (38.5%) being the most prevalent subgenotype followed by HBV/A1. The major mutations affecting HBeAg expression includes the A1762T/G1764A (13.6%), G1896A (22%) and G1862T mutation (33.9%) which was predominantly associated with HBV/A1. Moreover, the prevalence of G1896A was considerably high among the HBeAg negative HIV/HBV co-infected subjects compared to HBV mono-infection. The main amino acid substitutions within the MHC class II restricted T-cell epitope of HBcAg includes the T12S (15.8%) and T67N (12.3%) mutation and the V27I (10.5%) mutation in the MHC class I restricted T-cell epitope. PreS1/S2 deletion was detected in 3 isolates with all harboring the BCP double mutation. Furthermore, the frequently occurring mutations in the major hydrophilic loop of the S gene include the T125M, A128V and M133I/L. Therefore, this study is the first from India to report useful information on the molecular heterogeneity of the HBV strains circulating among the treatment naive HIV/HBV co-infected population and is thus clinically relevant.
Collapse
Affiliation(s)
- Debraj Saha
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, West Bengal, India
| | - Ananya Pal
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, West Bengal, India
| | - Avik Biswas
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, West Bengal, India
| | - Rajesh Panigrahi
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Neelakshi Sarkar
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, West Bengal, India
| | - Dipanwita Das
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, West Bengal, India
| | - Jayeeta Sarkar
- Calcutta School of Tropical Medicine, Kolkata, West Bengal, India
| | | | - Bibhuti Saha
- Calcutta School of Tropical Medicine, Kolkata, West Bengal, India
| | - Sekhar Chakrabarti
- National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Runu Chakravarty
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, Kolkata, West Bengal, India
- * E-mail:
| |
Collapse
|
44
|
Pourkarim MR, Vergote V, Amini-Bavil-Olyaee S, Sharifi Z, Sijmons S, Lemey P, Maes P, Alavian SM, Van Ranst M. Molecular characterization of hepatitis B virus (HBV) strains circulating in the northern coast of the Persian Gulf and its comparison with worldwide distribution of HBV subgenotype D1. J Med Virol 2014; 86:745-57. [PMID: 24532489 DOI: 10.1002/jmv.23864] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2013] [Indexed: 12/17/2022]
Abstract
Iran is a large country that covers the northern coast of the Persian Gulf. Iranian residents of this coastal region interact closely with people from neighboring countries because of historical and cultural relationships, as well as economic activities. In addition, the inhabitants of this border region have experienced several wars, which have affected public health infrastructures. This study characterized for the first time, the evolution of the full-length genome of HBV strains in asymptomatic carrier patients living in this particular region. In addition, this study was compared and complemented by a comprehensive evolutionary analysis of the worldwide geographical distribution of HBV subgenotype D1. Evolutionary analysis demonstrates that patients living in the northern coast of the Persian Gulf are mainly infected with HBV subgenotype D1, subtype ayw2. Specific mutations related to advanced liver disease were found more frequently in these strains compared to other strains isolated from asymptomatic carriers from other regions of Iran. This global comprehensive analysis showed that HBV subgenotype D1 strains have a worldwide distribution and that human mobility and immigration had a large impact on dispersal of HBV subgenotype D1, subtype ayw2 in Middle Eastern countries such as Iran, Syria, and Turkey. In addition to association of subtype ayw2 with subgenotype D1, it was demonstrated that other HBV subtypes like adw2, ayw1, and ayw3 are associated with HBV subgenotype D1 in different regions of the world. This study also revealed a remarkable distribution of subgenotype D1, subtype ayw4 although this particular subtype is associated with subgenotype D4 of HBV in European countries.
Collapse
Affiliation(s)
- Mahmoud Reza Pourkarim
- Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium; Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Drositis I, Bertsias A, Lionis C, Kouroumalis E. Epidemiology and molecular analysis of hepatitis A, B and C in a semi-urban and rural area of Crete. Eur J Intern Med 2013; 24:839-45. [PMID: 23988264 DOI: 10.1016/j.ejim.2013.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/10/2013] [Accepted: 08/03/2013] [Indexed: 02/08/2023]
Abstract
AIM An observational seroepidemiological study was carried out in a well-defined primary-care district on the island of Crete in order to determine the recent endemicity of viral hepatitis in Cretan-population. SETTING AND PARTICIPANTS The setting consisted of a semi-urban group and a remote & rural group. Serum samples were collected from 876 subjects (437 males, 439 females) aged 15 years or above. Subjects were randomly selected from the permanent population of the area that consisted of 5705 individuals. The aim was to measure the prevalence of selected viral-hepatitis markers. RESULTS Hepatitis B surface-antigen (HBsAg) was found positive in twenty-nine individuals, (3.3%). Antibodies to hepatitis B virus core-antigen (HBcAb) were detected in 287 subjects (32.8%) and antibodies to hepatitis C virus (anti-HCV) were detected in nineteen subjects (2.2%). Seropositivities for the semi-urban group were: 3.4%, 19.1%, 2.1% and 3.2%, 48.8%, 2.2% in remote & rural group respectively. Virtually, all subjects >45 years old were seropositive for antibodies to hepatitis A, whereas approximately 80% of those in the 15-44 age-group were found to be seropositive. CONCLUSION A threefold increase in the HBV exposure and carrier proportion was found in Cretan native-population and in rural-areas compared to older studies carried out in other rural-populations of the island. It is still unknown whether the recent economic crisis or the demographic changes in Cretan-population contributed to these findings. HCV endemicity remains relatively constant, however an alteration of hepatitis C genotypes was observed. Exposure to HAV was found to be higher in remote and rural areas compared to semi-urban areas.
Collapse
Affiliation(s)
- I Drositis
- Arkalochori Health Centre-Venizeleio General Hospital of Heraklion, Crete, Greece.
| | | | | | | |
Collapse
|
46
|
Bayesian phylogeography of Crimean-Congo hemorrhagic fever virus in Europe. PLoS One 2013; 8:e79663. [PMID: 24223988 PMCID: PMC3817137 DOI: 10.1371/journal.pone.0079663] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/24/2013] [Indexed: 11/19/2022] Open
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a zoonosis mainly transmitted by ticks that causes severe hemorrhagic fever and has a mortality rate of 5-60%. The first outbreak of CCHF occurred in the Crimean peninsula in 1944-45 and it has recently emerged in the Balkans and eastern Mediterranean. In order to reconstruct the origin and pathway of the worldwide dispersion of the virus at global and regional (eastern European) level, we investigated the phylogeography of the infection by analysing 121 publicly available CCHFV S gene sequences including two recently characterised Albanian isolates. The spatial and temporal phylogeny was reconstructed using a Bayesian Markov chain Monte Carlo approach, which estimated a mean evolutionary rate of 2.96 x 10-4 (95%HPD=1.6 and 4.7 x 10-4) substitutions/site/year for the analysed fragment. All of the isolates segregated into seven highly significant clades that correspond to the known geographical clades: in particular the two new isolates from northern Albania clustered significantly within the Europe 1 clade. Our phylogeographical reconstruction suggests that the global CCHFV clades originated about one thousand years ago from a common ancestor probably located in Africa. The virus then spread to Asia in the XV century and entered Europe on at least two occasions: the first in the early 1800s, when a still circulating but less or non-pathogenic virus emerged in Greece and Turkey, and the second in the early 1900s, when a pathogenic CCHFV strain began to spread in eastern Europe. The most probable location for the origin of this European clade 1 was Russia, but Turkey played a central role in spreading the virus throughout Europe. Given the close proximity of the infected areas, our data suggest that the movement of wild and domestic ungulates from endemic areas was probably the main cause of the dissemination of the virus in eastern Europe.
Collapse
|
47
|
Ciccozzi M, Ciccaglione AR, Lo Presti A, Equestre M, Cella E, Ebranati E, Gabanelli E, Villano U, Bruni R, Yalcinkaya T, Tanzi E, Zehender G. Evolutionary dynamics of HBV-D1 genotype epidemic in Turkey. J Med Virol 2013; 86:109-16. [DOI: 10.1002/jmv.23740] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2013] [Indexed: 12/26/2022]
Affiliation(s)
- Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases; Italian Institute of Health; Rome Italy
| | - Anna Rita Ciccaglione
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit; Italian Institute of Health; Rome Italy
| | - Alessandra Lo Presti
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases; Italian Institute of Health; Rome Italy
| | - Michele Equestre
- Department of Cell Biology and Neurosciences; Italian Institute of Health; Rome Italy
| | - Eleonora Cella
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases; Italian Institute of Health; Rome Italy
| | - Erika Ebranati
- Department of Biomedical and Clinical Sciences, Infectious Diseases and Immunopathology Section; ‘L. Sacco’ Hospital, University of Milan; Milan Italy
| | - Elena Gabanelli
- Department of Biomedical and Clinical Sciences, Infectious Diseases and Immunopathology Section; ‘L. Sacco’ Hospital, University of Milan; Milan Italy
| | - Umbertina Villano
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit; Italian Institute of Health; Rome Italy
| | - Roberto Bruni
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit; Italian Institute of Health; Rome Italy
| | | | - Elisabetta Tanzi
- Department of Public Health, Microbiology and Virology; University of Milan; Milano Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences, Infectious Diseases and Immunopathology Section; ‘L. Sacco’ Hospital, University of Milan; Milan Italy
| |
Collapse
|
48
|
Pourkarim MR, Sharifi Z, Soleimani A, Amini-Bavil-Olyaee S, Elsadek Fakhr A, Sijmons S, Vercauteren J, Karimi G, Lemey P, Maes P, Alavian SM, Van Ranst M. Evolutionary analysis of HBV “S” antigen genetic diversity in Iranian blood donors: A nationwide study. J Med Virol 2013; 86:144-55. [DOI: 10.1002/jmv.23798] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Mahmoud Reza Pourkarim
- Department of Microbiology and Immunology; Laboratory of Clinical and Epidemiological Virology; Rega Institute for Medical Research; KU Leuven Leuven Belgium
- Blood Transfusion Research Center; High Institute for Research and Education in Transfusion Medicine; Tehran Iran
| | - Zohre Sharifi
- Blood Transfusion Research Center; High Institute for Research and Education in Transfusion Medicine; Tehran Iran
| | - Ali Soleimani
- Blood Transfusion Research Center; High Institute for Research and Education in Transfusion Medicine; Tehran Iran
| | - Samad Amini-Bavil-Olyaee
- Department of Molecular Microbiology and Immunology; Keck School of Medicine; University of Southern California; Harlyne J. Norris Cancer Research Tower; Los Angeles CA 90033
| | - Ahmed Elsadek Fakhr
- Department of Microbiology and Immunology; Laboratory of Clinical and Epidemiological Virology; Rega Institute for Medical Research; KU Leuven Leuven Belgium
| | - Steven Sijmons
- Department of Microbiology and Immunology; Laboratory of Clinical and Epidemiological Virology; Rega Institute for Medical Research; KU Leuven Leuven Belgium
| | - Jurgen Vercauteren
- Department of Microbiology and Immunology; Laboratory of Clinical and Epidemiological Virology; Rega Institute for Medical Research; KU Leuven Leuven Belgium
| | - Gharib Karimi
- Blood Transfusion Research Center; High Institute for Research and Education in Transfusion Medicine; Tehran Iran
| | - Philippe Lemey
- Department of Microbiology and Immunology; Laboratory of Clinical and Epidemiological Virology; Rega Institute for Medical Research; KU Leuven Leuven Belgium
| | - Piet Maes
- Department of Microbiology and Immunology; Laboratory of Clinical and Epidemiological Virology; Rega Institute for Medical Research; KU Leuven Leuven Belgium
| | - Seyed Moayed Alavian
- Department of Molecular Microbiology and Immunology; Keck School of Medicine; University of Southern California; Harlyne J. Norris Cancer Research Tower; Los Angeles CA 90033
- Middle East Liver Disease Clinics; Tehran Iran
| | - Marc Van Ranst
- Department of Microbiology and Immunology; Laboratory of Clinical and Epidemiological Virology; Rega Institute for Medical Research; KU Leuven Leuven Belgium
| |
Collapse
|
49
|
Ouneissa R, Bahri O, Ben Yahia A, Touzi H, Azouz MM, Ben Mami N, Triki H. Evaluation of PCR-RFLP in the Pre-S Region as Molecular Method for Hepatitis B Virus Genotyping. HEPATITIS MONTHLY 2013; 13:e11781. [PMID: 24348634 PMCID: PMC3842526 DOI: 10.5812/hepatmon.11781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/01/2013] [Accepted: 10/06/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is a public health problem in developing countries. HBV genotypes play major role in the evolution of infection since they were involved in different clinical presentations and response to treatment. OBJECTIVES This study was conducted to evaluate the efficiency of restriction fragment length polymorphism (RFLP) analysis for HBV genotyping. PATIENTS AND METHODS We investigated 98 samples collected from patients chronically infected with HBV. HBV genotypes were determined by analysis of patterns obtained after amplification in Pre-S region and digestion of the amplicon by two endonucleases AvaII and DpnII. Obtained results were confirmed by partial sequencing in the same region. RESULTS Two different HBV genotypes were detected in this study, Genotype D (in 95. 9%) and Genotype A (in 4.1%). Seventy-four samples (75.5%) were successfully genotyped with RFLP analysis and all classified as genotype D. The remaining 24 samples (24.5%) which were un-genotyped by RFLP analysis, were classified by partial sequencing of the pre-S region as HBV genotype D (20 samples, 20.4%) and genotype A (4 samples, 4.1%). Atypical profiles were significantly associated with advanced liver disease (P = 0.001) as well as older age (P < 0.05). CONCLUSIONS Several previous studies used PCR-RFLP to genotype HBV; however, we showed the high risk to obtain atypical profiles, especially in advanced stages of chronic infection, with as results difficulties to genotype the virus. These profiles resulted from the accumulation of mutations during natural course of infection resulting in a modification in restriction sites for enzymes. So, we recommended completing the investigation by partial sequencing to confirm obtained results.
Collapse
Affiliation(s)
- Rim Ouneissa
- Laboratory of Clinical Virology, Institute Pasteur de Tunis, Tunis, Tunisia
| | - Olfa Bahri
- Laboratory of Clinical Virology, Institute Pasteur de Tunis, Tunis, Tunisia
- Corresponding author: Olfa Bahri, Laboratory of Clinical Virology, Institute Pasteur de Tunis, Tunis, BP 1002, Tunisia. Tel: +216-98334999, Fax: +216-71791833, E-mail:
| | - Ahlem Ben Yahia
- Laboratory of Clinical Virology, Institute Pasteur de Tunis, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, Institute Pasteur de Tunis, Tunis, Tunisia
| | | | - Nabyl Ben Mami
- Department of Gastroenterology, Hospital La Rabta, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, Institute Pasteur de Tunis, Tunis, Tunisia
| |
Collapse
|
50
|
Barbini L, Elizalde M, Torres C, Campos R. Molecular epidemiology and genetic diversity of hepatitis B virus in Mar del Plata city, Argentina. INFECTION GENETICS AND EVOLUTION 2013; 19:152-63. [PMID: 23871776 DOI: 10.1016/j.meegid.2013.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 12/13/2022]
Abstract
The aim of this work was to describe the current molecular epidemiology and genetic diversity of HBV in Mar del Plata, an important Argentinean touristic city. The phylogenetic analysis of 29 HBV DNA positive serum samples showed that F1b was the predominant subgenotype (sgt, 62.1%), followed by sgt A2 (13.8%) and sgt F4, gt D and gt G (6.9% each). Among anti-HBc IgM positive samples, 75.0% were sgt F1b, followed by sgt F4 (12.5%), sgt A2 (6.25%) and sgt D (6.25%). Three recombinant full length genomes were found: two G/F1b (some of the first gt G detected in Argentina) and one F4/D2. The circulation of clinical important mutations in the city was described. Mutations at the HBsAg were detected in 34.5% of the analyzed samples, associated with laboratory diagnosis and antiviral treatment failures, immune escape and hepatocellular carcinoma. Most of the samples presented wild type BCP/PC sequences. Coalescence analysis for the most prevalent sgt F1b estimated that the diversification mainly occured during mid '90s and the tMRCA was estimated in 1987. Finally, the high presence of the autochthonous sgt F1b, associated with the anti-HBc IgM positive infection and its present-day diversification process, shows the strong impact of internal human migratory movements into the current population of Mar del Plata.
Collapse
Affiliation(s)
- Luciana Barbini
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4(to) piso. (1113), Ciudad Autónoma de Buenos Aires, Argentina.
| | | | | | | |
Collapse
|