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Sant’Anna TBF, Martins TLS, dos Santos Carneiro MA, Teles SA, Caetano KAA, de Araujo NM. First Detection of Hepatitis B Virus Subgenotype A5, and Characterization of Occult Infection and Hepatocellular Carcinoma-Related Mutations in Latin American and African Immigrants in Brazil. Int J Mol Sci 2024; 25:8602. [PMID: 39201291 PMCID: PMC11354843 DOI: 10.3390/ijms25168602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 09/02/2024] Open
Abstract
This study aims to characterize the molecular profile of the hepatitis B virus (HBV) among socially vulnerable immigrants residing in Brazil to investigate the introduction of uncommon HBV strains into the country. Serum samples from 102 immigrants with positive serology for the HBV core antibody (anti-HBc) were tested for the presence of HBV DNA by PCR assays. Among these, 24 were also positive for the HBV surface antigen (HBsAg). The full or partial genome was sequenced to determine genotype by phylogenetic analysis. Participants were from Haiti (79.4%), Guinea-Bissau (11.8%), Venezuela (7.8%), and Colombia (1%). Of the 21 HBV DNA-positive samples, subgenotypes A1 (52.4%), A5 (28.6%), E (9.5%), F2 (4.8%), and F3 (4.8%) were identified. Among the 78 HBsAg-negative participants, four were positive for HBV DNA, resulting in an occult HBV infection rate of 5.1%. Phylogenetic analysis suggested that most strains were likely introduced to Brazil by migration. Importantly, 80% of A5 sequences had the A1762T/G1764A double mutation, linked to an increased risk of hepatocellular carcinoma development. In conclusion, this study is the first report of HBV subgenotype A5 in Brazil, shedding new light on the diversity of HBV strains circulating in the country. Understanding the genetic diversity of HBV in immigrant communities can lead to better prevention and control strategies, benefiting both immigrants and wider society.
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Affiliation(s)
| | | | | | - Sheila Araujo Teles
- Faculty of Nursing, Federal University of Goiás, Goiania 74605-080, Brazil; (T.L.S.M.); (S.A.T.); (K.A.A.C.)
| | | | - Natalia Motta de Araujo
- Laboratory of Molecular Virology and Parasitology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
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Phinius BB, Anderson M, Gobe I, Mokomane M, Choga WT, Phakedi B, Ratsoma T, Mpebe G, Makhema J, Shapiro R, Lockman S, Musonda R, Moyo S, Gaseitsiwe S. High Prevalence of Hepatitis B Virus Drug Resistance Mutations to Lamivudine among People with HIV/HBV Coinfection in Rural and Peri-Urban Communities in Botswana. Viruses 2024; 16:592. [PMID: 38675933 PMCID: PMC11054684 DOI: 10.3390/v16040592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
(1) Background: We aimed to determine the prevalence of hepatitis B virus (HBV) resistance-associated mutations (RAMs) in people with HBV and human immunodeficiency virus (HBV/HIV) in Botswana. (2) Methods: We sequenced HBV deoxyribonucleic acid (DNA) from participants with HBV/HIV from the Botswana Combination Prevention Project study (2013-2018) using the Oxford Nanopore GridION platform. Consensus sequences were analyzed for genotypic and mutational profiles. (3) Results: Overall, 98 HBV sequences had evaluable reverse transcriptase region coverage. The median participant age was 43 years (IQR: 37, 49) and 66/98 (67.4%) were female. Most participants, i.e., 86/98 (87.8%) had suppressed HIV viral load (VL). HBV RAMs were identified in 61/98 (62.2%) participants. Most RAMs were in positions 204 (60.3%), 180 (50.5%), and 173 (33.3%), mostly associated with lamivudine resistance. The triple mutations rtM204V/L180M/V173L were the most predominant (17/61 [27.9%]). Most participants (96.7%) with RAMs were on antiretroviral therapy for a median duration of 7.5 years (IQR: 4.8, 10.5). Approximately 27.9% (17/61) of participants with RAMs had undetectable HBV VL, 50.8% (31/61) had VL < 2000 IU/mL, and 13/61 (21.3%) had VL ≥ 2000 IU/mL. (4) Conclusions: The high prevalence of lamivudine RAMs discourages the use of ART regimens with 3TC as the only HBV-active drug in people with HIV/HBV.
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Affiliation(s)
- Bonolo B. Phinius
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Private Bag UB 0022, Gaborone, Botswana; (I.G.); (M.M.)
| | - Motswedi Anderson
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
| | - Irene Gobe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Private Bag UB 0022, Gaborone, Botswana; (I.G.); (M.M.)
| | - Margaret Mokomane
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Private Bag UB 0022, Gaborone, Botswana; (I.G.); (M.M.)
| | - Wonderful T. Choga
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Private Bag UB 0022, Gaborone, Botswana; (I.G.); (M.M.)
| | - Basetsana Phakedi
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
| | - Tsholofelo Ratsoma
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
| | - Gorata Mpebe
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
| | - Joseph Makhema
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Roger Shapiro
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shahin Lockman
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rosemary Musonda
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
| | - Sikhulile Moyo
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Private Bag UB 0022, Gaborone, Botswana; (I.G.); (M.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Simani Gaseitsiwe
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (B.B.P.); (M.A.); (G.M.); (J.M.); (R.S.); (S.L.); (R.M.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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3
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Sun B, Andrades Valtueña A, Kocher A, Gao S, Li C, Fu S, Zhang F, Ma P, Yang X, Qiu Y, Zhang Q, Ma J, Chen S, Xiao X, Damchaabadgar S, Li F, Kovalev A, Hu C, Chen X, Wang L, Li W, Zhou Y, Zhu H, Krause J, Herbig A, Cui Y. Origin and dispersal history of Hepatitis B virus in Eastern Eurasia. Nat Commun 2024; 15:2951. [PMID: 38580660 PMCID: PMC10997587 DOI: 10.1038/s41467-024-47358-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
Hepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We present 34 ancient HBV genomes dating between approximately 5000 to 400 years ago sourced from 17 sites across Eastern Eurasia. Ten sequences have full coverage, and only two sequences have less than 50% coverage. Our results suggest a potential origin of genotypes B and D in Eastern Asia. We observed a higher level of HBV diversity within Eastern Eurasia compared to Western Eurasia between 5000 and 3000 years ago, characterized by the presence of five different genotypes (A, B, C, D, WENBA), underscoring the significance of human migrations and interactions in the spread of HBV. Our results suggest the possibility of a transition from non-recombinant subgenotypes (B1, B5) to recombinant subgenotypes (B2 - B4). This suggests a shift in epidemiological dynamics within Eastern Eurasia over time. Here, our study elucidates the regional origins of prevalent genotypes and shifts in viral subgenotypes over centuries.
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Affiliation(s)
- Bing Sun
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Arthur Kocher
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Shizhu Gao
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China
| | - Chunxiang Li
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Shuang Fu
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Xuan Yang
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yulan Qiu
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Quanchao Zhang
- School of archaeology, Jilin University, Changchun, 130021, China
| | - Jian Ma
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Shan Chen
- School of Archaeology and Museology, Liaoning University, Shenyang, 110136, China
| | - Xiaoming Xiao
- School of Archaeology and Museology, Liaoning University, Shenyang, 110136, China
| | | | - Fajun Li
- School of Sociology and Anthropology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Alexey Kovalev
- Department of archaeological heritage preservation, Institute of Archaeology of Russian Academy of Sciences, Moscow, 117292, Russia
| | - Chunbai Hu
- Institute of Cultural Relics and Archaeology, Inner Mongolia Autonomous Region, Hohhot, 010010, China
| | - Xianglong Chen
- Institute of Archaeology, Chinese Academy of Social Sciences, Beijing, 100101, China
| | - Lixin Wang
- Research Center for Chinese Frontier Archaeology of Jilin University, Jilin University, Changchun, 130012, China
| | - Wenying Li
- Xinjiang Institute of Cultural Relics and Archaeology, Ürümqi, 830011, China
| | - Yawei Zhou
- School of History, Zhengzhou University, Zhengzhou, 450066, China
| | - Hong Zhu
- Research Center for Chinese Frontier Archaeology of Jilin University, Jilin University, Changchun, 130012, China
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, 130012, China.
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4
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Silcocks M, Dunstan SJ. Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history. Commun Biol 2023; 6:1037. [PMID: 37833496 PMCID: PMC10575886 DOI: 10.1038/s42003-023-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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5
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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: 2.5] [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.
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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
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6
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Villano U, Mataj E, Dorrucci M, Farchi F, Pirone C, Valdarchi C, Equestre M, Madonna E, Bruni R, Pisani G, Martina A, Simeoni M, Iaiani G, Ciccozzi M, Ciccaglione AR, Conti F, Ceccarelli F, Lo Presti A. Molecular Characterization of Hepatitis B Virus Infection in a Patient with Cutaneous Lupus Erythematosus. Diagnostics (Basel) 2022; 12:2866. [PMID: 36428926 PMCID: PMC9689093 DOI: 10.3390/diagnostics12112866] [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: 08/05/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a serious global health problem. Patients with autoimmune diseases, such as Lupus Erythematosus, are exposed to a higher risk of acquiring infections. In this study, a molecular characterization, genomic investigation of the Hepatitis B virus, polymerase (P) and surface (S) genes, from a patient affected by Cutaneous Lupus Erythematosus (CLE), was presented. Viral DNA was extracted from 200 μL of serum, and the HBV-DNA was amplified by real-time polymerase chain reaction (PCR) with the Platinum Taq DNA Polymerase. The PCR products were purified and sequencing reactions were performed. A phylogenetic analysis was performed through maximum likelihood and Bayesian approaches. The HBV CLE isolate was classified as sub-genotype D3 and related to other Italian HBV D3 genomes, and some from foreign countries. No drug resistant mutations were identified. One mutation (a.a. 168 M) was located in the last part of the major hydrophilic region (MHR) of the surface antigen (HBsAg). Moreover, three sites (351G, 526Y, 578C) in the polymerase were exclusively present in the CLE patient. The mutations identified exclusively in the HBsAg of our CLE patient may have been selected because of the Lupus autoantibodies, which are characteristic in the Lupus autoimmune disease, using a possible molecular mimicry mechanism.
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Affiliation(s)
- Umbertina Villano
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Elida Mataj
- Instituti i Shendetit Publik (ISHP), Alessander Moisiu No. 80, Tirane, Albania
| | - Maria Dorrucci
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesca Farchi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Carmelo Pirone
- Lupus Clinic, Rheumatology, Dipartimento di Scienze Cliniche, Internistiche, Anestesiologiche e Cardiovascolari, Sapienza Università, 00185 Rome, Italy
| | - Catia Valdarchi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Michele Equestre
- Department of Cell Biology and Neuroscience, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Elisabetta Madonna
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Giulio Pisani
- Center for Immunobiological Research and Evaluation, National Institute of Health, 00161 Rome, Italy
| | - Antonio Martina
- Center for Immunobiological Research and Evaluation, National Institute of Health, 00161 Rome, Italy
| | - Matteo Simeoni
- Center for Immunobiological Research and Evaluation, National Institute of Health, 00161 Rome, Italy
| | - Giancarlo Iaiani
- Department of Tropical and Infectious Diseases, Aou Policlinico Umberto I, 00185 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | | | - Fabrizio Conti
- Lupus Clinic, Rheumatology, Dipartimento di Scienze Cliniche, Internistiche, Anestesiologiche e Cardiovascolari, Sapienza Università, 00185 Rome, Italy
| | - Fulvia Ceccarelli
- Lupus Clinic, Rheumatology, Dipartimento di Scienze Cliniche, Internistiche, Anestesiologiche e Cardiovascolari, Sapienza Università, 00185 Rome, Italy
| | - Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
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7
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Dagnew M, Moges F, Tiruneh M, Million Y, Gelaw A, Adefris M, Belyhun Y, Liebert UG, Maier M. Molecular diversity of hepatitis B virus among pregnant women in Amhara National Regional State, Ethiopia. PLoS One 2022; 17:e0276687. [PMID: 36378635 PMCID: PMC9665361 DOI: 10.1371/journal.pone.0276687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022] Open
Abstract
Background Despite the availability of effective vaccines and treatments for hepatitis B virus (HBV), it continues to be a major public health problem in sub-Saharan Africa including Ethiopia. Routine screening for HBV in pregnant women is widely recommended, but there is lack of screening for HBV during pregnancy in Ethiopia. Therefore, this study aimed to assess viral load, and genetic diversity among pregnant women in the Amhara National Regional State, Ethiopia. Materials and methods Hepatitis B surface antigen (HBsAg) testing was performed on 1846 pregnant women, 85 of who tested positive were included in this study. HBV DNA was isolated from 85 positive sera, and the partial surface/polymerase gene was amplified and sequenced. HBV genotypes, sub-genotypes, serotypes and mutations in surface genes and polymerase were studied. Results Out of 85 pregnant women`s HBsAg positive sera, 59(69.4%) had detectable viral DNA. The median viral load was 3.4 log IU/ml ranging from 2.6 to7.6 and 46 samples were successfully sequenced and genotyped. Genotypes A and D were identified in 39 (84.8%) and 7 (15.2%); respectively. All genotype A isolates were further classified into sub-genotype A1 and serotype adw2 (84.8%) whereas genotype D isolates were further classified into three sub genotypes; 2 (4.3%) D2, 1(2.2%) D4, and 4 (8.7%) D10 with serotypes ayw2 (10.9%), and ayw3 (4.3%). There were 19 (41.3%) surface gene mutations in the major hydrophilic region (MHR). Six (13.1%) of them were discovered in MHR`s `a’-determinant region. Six polymerase gene mutations (13%) were identified. Conclusion Genotype A was the predominant genotype in the Amhara National Regional State. The surface and polymerase gene mutations identified in this study may lead to immune therapy failure, diagnostics escape and drug resistance. Thus, the data generated in this study will contribute to the planning of HBV diagnosis, vaccination and treatment, and most importantly to the prevention of vertical transmission of HBV in Ethiopia. Therefore, further molecular studies on HBV are warranted and continuous surveillance is important for patient management and for the prevention and control of HBV infection in the country.
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Affiliation(s)
- Mulat Dagnew
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- Department of Virology, Institute of Medical Microbiology and Virology, Leipzig University, Leipzig, Germany
- * E-mail:
| | - Feleke Moges
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Moges Tiruneh
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Yihenew Million
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Aschalew Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mulat Adefris
- Department of Gynecology and Obstetrics, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Yeshambel Belyhun
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- Department of Virology, Institute of Medical Microbiology and Virology, Leipzig University, Leipzig, Germany
| | - Uwe G. Liebert
- Department of Virology, Institute of Medical Microbiology and Virology, Leipzig University, Leipzig, Germany
| | - Melanie Maier
- Department of Virology, Institute of Medical Microbiology and Virology, Leipzig University, Leipzig, Germany
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8
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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9
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Araújo SDR, Malheiros AP, Sarmento VP, Nunes HM, Freitas PEB. Molecular investigation of occult hepatitis B virus infection in a reference center in Northern Brazil. Braz J Infect Dis 2022; 26:102367. [PMID: 35598631 PMCID: PMC9387453 DOI: 10.1016/j.bjid.2022.102367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/30/2022] [Indexed: 11/18/2022] Open
Abstract
The goal of this study was to investigate the prevalence of occult HBV infection in a reference center for the Northern Brazil from 2005 to 2015 and to identify mutations associated with occult hepatitis B. Molecular analysis was performed on 110 serum samples in which anti-HBc was the only positive serological marker. Regions of the HBV genome were amplified by polymerase chain reaction to detect HBV DNA. A prevalence of 4.1% (793/18,889) for anti-HBc alone was identified. Molecular analysis revealed a prevalence of occult HBV infection of 0.04%. HBV DNA detected were identified in individuals who underwent hemodialysis, infected with the hepatitis C virus and from area of high endemicity for HBV. Direct DNA nucleotide sequencing and phylogenetic analysis identified that genotypes A and D and mutations E164D, I195M, P217L and P120S were associated with occult HBV infection in the S gene. This study contributed with epidemiological and molecular information on Northern Brazil samples with a suggestive profile of occult HBV infection in addition to reinforcing the importance of molecular diagnosis in this type of infection.
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10
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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: 4] [Impact Index Per Article: 1.3] [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.
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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
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11
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Araujo NM, Osiowy C. Hepatitis B Virus Genotype G: The Odd Cousin of the Family. Front Microbiol 2022; 13:872766. [PMID: 35432294 PMCID: PMC9009205 DOI: 10.3389/fmicb.2022.872766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
With a widespread distribution but low prevalence worldwide, the hepatitis B virus (HBV) genotype G (HBV/G) is a recently described genotype for which the origin and biology are poorly understood. Some unique features make HBV/G the most peculiar of all genotypes. In this review, we reflect on the major milestones in HBV/G research, highlighting the main aspects of its discovery, molecular epidemiology, and virological and clinical characteristics. We also illustrate common pitfalls in the routine detection, which may lead to underestimated rates of HBV/G infection. Large-scale analysis of data from dozens of articles was further performed, with the aim of gaining comprehensive insights into the epidemiological aspects of HBV/G. Finally, we point out recent findings on HBV/G origins and discuss new perspectives regarding the evolutionary history of HBV/G and the plausibility of an African geographic re-emergence of this genotype.
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Affiliation(s)
- Natalia M. Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Carla Osiowy
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- *Correspondence: Carla Osiowy,
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12
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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.
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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
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13
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Wolf JM, Mazeto TK, Pereira VRZB, Simon D, Lunge VR. Recent molecular evolution of hepatitis B virus genotype F in Latin America. Arch Virol 2022; 167:597-602. [DOI: 10.1007/s00705-022-05376-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/17/2021] [Indexed: 11/24/2022]
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14
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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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15
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Wolf JM, Pereira VRZB, Simon D, Lunge VR. Temporal and geographic spreading of hepatitis B virus genotype A (HBV-A) in Brazil and the Americas. J Viral Hepat 2021; 28:1130-1140. [PMID: 33932242 DOI: 10.1111/jvh.13527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/17/2021] [Indexed: 12/27/2022]
Abstract
Hepatitis B virus genotype A (HBV-A) is disseminated in different countries around the world. It presents a high genetic diversity and is classified into seven subgenotypes (A1-A7). HBV-A1 and HBV-A2 are the most frequent and spread in almost all American countries. This study aimed to evaluate the molecular epidemiology of these two subgenotypes, with a special focus on the temporal and geographic spreading in the Americas and Brazil. Bayesian coalescent analyses with HBV-A1 and HBV-A2 whole-genome sequences were performed to study viral phylodynamic and phylogeography. HBV-A1 evolutionary history demonstrated that it was initially disseminated from Africa to other continents probably after the 1400s and mainly in the 17th-18th centuries. The whole viral population grew between the 1700s-1900s and then reached a stationary phase. In Brazil, HBV-A1 common ancestors dated back to the 1600s with successive introductions between the 17th-18th centuries. In contrast, HBV-A2 spread from Europe to other continents after the 1800s, with an increase in the viral population over decades. It was introduced in the 20th century in America and between the 1950s-1970s in Brazil, presenting a high increase in the viral population from the 1970s to the 1980s. The circulation continents for HBV-A1 are Africa and America, while for HBV-A2 are Europe and America. HBV-A is one of the predominant genotypes in America (including Brazil) because of the early introduction by human migration processes of the subgenotypes A1 and A2 between the 16th and 20th centuries and the continuous spreading inside the continent over time.
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Affiliation(s)
- Jonas Michel Wolf
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
| | | | - Daniel Simon
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
| | - Vagner Ricardo Lunge
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
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16
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Wolf JM, Pereira VRZB, Simon D, Lunge VR. Evolutionary history of hepatitis B virus genotype H. J Med Virol 2021; 93:4004-4009. [PMID: 32852054 DOI: 10.1002/jmv.26463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/27/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022]
Abstract
Hepatitis B virus genotype H (HBV-H) molecular evolution was studied by comparing all published whole-genome sequences. Bayesian coalescent analysis was performed to estimate phylogenetic relationships, time to the most recent common ancestor (tMRCA), and viral population dynamics along the time. Phylogenetic tree demonstrated two main clades or lineages: HBV-H I (with sequences from Central and North America) and HBV-H II (with sequences from North and South America, and Asia). HBV-H II had more genome sequences (n = 26; 83.9%), including one specific subclade with all sequences outside of the Americas. Overall HBV-H tMRCA dated back to 1933 (95% highest posterior density interval [HPD 95%]: 1875-1957) with a very probable origin in Mexico and posterior dissemination to other American and Asian countries. The temporal analysis demonstrated that HBV-H I spread only in Mexico and the neighbor country of Nicaragua probably in the 1960s to the 1970s (1968; HPD 95%: 1908-1981), while HBV-II disseminated to other American and Asian countries around one decade later (1977; HPD 95%: 1925-1985). The phylogeographic analysis reinforced the Mexican origin of this genotype. The whole HBV-H population increased from the 1980s to the 2000s. In conclusion, HBV-H has two main lineages with a common origin in Mexico approximately nine decades ago.
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Affiliation(s)
- Jonas Michel Wolf
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil
| | | | - Daniel Simon
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil
| | - Vagner Ricardo Lunge
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil
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17
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Hepatitis B virus genotypes in Brazil: Introduction and dissemination. INFECTION GENETICS AND EVOLUTION 2021; 93:104936. [PMID: 34023512 DOI: 10.1016/j.meegid.2021.104936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022]
Abstract
Hepatitis B is a viral infectious disease highly spread worldwide with a long evolutionary history associated with human migrations through the continents and countries. Hepatitis B virus (HBV) was disseminated probably from Africa and diverged into ten genotypes (HBV-A to HBV-J) distributed around the world. In Brazil, almost all HBV genotypes were already reported, with a predominance of three ones: A (52.1%), D (36.8%), and F (7.7%). This review aimed to evaluate the introduction and dissemination of the main HBV genotypes and subgenotypes in Brazil over the last centuries to explain the current epidemic scenario. The highest frequency of HBV-A is a consequence of the introduction and spreading of HBV-A1 in the 16th to 19th centuries due to the African slave trade, but the more recent introduction of HBV-A2 from Europe also contributed to the current situation. HBV-D is the second most frequent genotype because it was consecutively introduced by migrations from Europe (mainly subgenotype D3, but also D2) and the Middle East (D1) in the 19th to 20th centuries. On contrary, HBV-F (F1a, F1b, F2a, F2b, F3, and F4) was disseminated by the Amerindians in all South American countries, including Brazil, by migrations inside the continent for more than three centuries ago. Other HBV genotypes are rare and eventually frequent in some human groups because of the dissemination by very specific epidemiological routes. In conclusion, the current scenario of the HBV epidemics is a consequence of the introduction and dissemination of some subgenotypes from the three main genotypes A, D, and F over the last five centuries.
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18
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Wolf JM, De Carli S, Pereira VRZB, Simon D, Lunge VR. Temporal evolution and global spread of hepatitis B virus genotype G. J Viral Hepat 2021; 28:393-399. [PMID: 33128240 DOI: 10.1111/jvh.13431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 09/09/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) infection is considered a major health problem in the world. HBV is classified into genotypes A to J disseminated worldwide. Genotypes A, D and F are the most frequent in the Western World, B and C are predominant in the East, and E, F, H and J are infrequent and restricted to specific regions. HBV-G is a rare genotype, but it has been detected in different continents. This study aimed to report the temporal evolution and global spread of HBV-G comparing whole-genome sequences of this genotype from different regions in the world. Bayesian coalescent analysis was performed to estimate the time to the most recent common ancestor (tMRCA) and the population dynamics in the last decades. The results demonstrated that tMRCA of all HBV-Gs dated back to 1855 (95% highest posterior density interval [HPD 95%]: 1778 - 1931). This genotype has a possible origin in North America and it was disseminated to other continents (South and Central America, Europe, Asia and Africa) more than one century later (around the 1970s). The viral population demonstrated constant spreading from 1855 to the 1980s, followed by an increase in the 1990s and reached a plateau after the 2000s. Wide spreading at the beginning of the 1990s was probably associated with the dissemination by highly sexual active groups and injecting drug users. In conclusion, the present study demonstrated that HBV-G was originated in the 19th century with main events of spread at the end of the 20th century.
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Affiliation(s)
- Jonas Michel Wolf
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, ULBRA, Universidade Luterana do Brasil, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
| | - Sílvia De Carli
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
| | | | - Daniel Simon
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, ULBRA, Universidade Luterana do Brasil, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
| | - Vagner Ricardo Lunge
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, ULBRA, Universidade Luterana do Brasil, Canoas, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Brazil
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19
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Araujo NM, Teles SA, Spitz N. Comprehensive Analysis of Clinically Significant Hepatitis B Virus Mutations in Relation to Genotype, Subgenotype and Geographic Region. Front Microbiol 2020; 11:616023. [PMID: 33381105 PMCID: PMC7767914 DOI: 10.3389/fmicb.2020.616023] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) is a highly variable DNA virus due to its unique life cycle, which involves an error-prone reverse transcriptase. The high substitution rate drives the evolution of HBV by generating genetic variants upon which selection operates. HBV mutants with clinical implications have been documented worldwide, indicating the potential for spreading and developing their own epidemiology. However, the prevalence of such mutants among the different HBV genotypes and subgenotypes has not been systematically analyzed. In the current study, we performed large-scale analysis of 6,479 full-length HBV genome sequences from genotypes A-H, with the aim of gaining comprehensive insights into the relationships of relevant mutations associated with immune escape, antiviral resistance and hepatocellular carcinoma (HCC) development with HBV (sub)genotypes and geographic regions. Immune escape mutations were detected in 10.7% of the sequences, the most common being I/T126S (1.8%), G145R (1.2%), M133T (1.2%), and Q129R (1.0%). HBV genotype B showed the highest rate of escape mutations (14.7%) while genotype H had no mutations (P < 0.001). HCC-associated mutations were detected in 33.7% of the sequences, with significantly higher frequency of C1653T, T1753V and A1762T/G1764A in genotype G than C (P < 0.001). The overall frequencies of lamivudine-, telbivudine-, adefovir-, and entecavir-resistant mutants were 7.3, 7.2, 0.5, and 0.2%, respectively, while only 0.05% showed reduced susceptibility to tenofovir. In particular, the highest frequency of lamivudine-resistant mutations was observed in genotype G and the lowest frequency in genotype E (32.5 and 0.3%; P < 0.001). The prevalence of HBV mutants was also biased by geographic location, with North America identified as one of the regions with the highest rates of immune escape, antiviral resistance, and HCC-associated mutants. The collective findings were discussed in light of natural selection and the known characteristics of HBV (sub)genotypes. Our data provide relevant information on the prevalence of clinically relevant HBV mutations, which may contribute to further improvement of diagnostic procedures, immunization programs, therapeutic protocols, and disease prognosis.
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Affiliation(s)
- Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Sheila A Teles
- Faculty of Nursing, Federal University of Goias, Goiânia, Brazil
| | - Natália Spitz
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
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20
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Pujol F, Jaspe RC, Loureiro CL, Chemin I. Hepatitis B virus American genotypes: Pathogenic variants ? Clin Res Hepatol Gastroenterol 2020; 44:825-835. [PMID: 32553521 DOI: 10.1016/j.clinre.2020.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) chronic infection is responsible for almost 900.000 deaths each year, due to cirrhosis or hepatocellular carcinoma (HCC). Ten HBV genotypes have been described (A-J). HBV genotype F and H circulate in America. HBV genotypes have been further classified in subgenotypes. There is a strong correlation between the genetic admixture of the American continent and the frequency of genotypes F or H: a high frequency of these genotypes is found in countries with a population with a higher ratio of Amerindian to African genetic admixture. The frequency of occult HBV infection in Amerindian communities from Latin America seems to be higher than the one found in other HBV-infected groups, but its association with American genotypes is unknown. There is growing evidence that some genotypes might be associated with a faster evolution to HCC. In particular, HBV genotype F has been implicated in a frequent and rapid progression to HCC. However, HBV genotype H has been associated to a less severe progression of disease. This study reviews the diversity and frequency of autochthonous HBV variants in the Americas and evaluates their association to severe progression of disease. Although no significant differences were found in the methylation pattern between different genotypes and subgenotypes of the American types, basal core promoter mutations might be more frequent in some subgenotypes, such as F1b and F2, than in other American subgenotypes or genotype H. F1b and probably F2 may be associated with a severe presentation of liver disease as opposed to a more benign course for subgenotype F4 and genotype H. Thus, preliminary evidence suggests that not all of the American variants are associated with a rapid progression to HCC.
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Affiliation(s)
- Flor Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela.
| | - Rossana C Jaspe
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela
| | - Isabelle Chemin
- INSERM U1052, CNRS 5286, Université de Lyon, Université Claude Bernard Lyon 1, centre Léon Bérard, centre de recherche en cancérologie de Lyon, 69000, Lyon, France
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21
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Tracing back hepatitis B virus genotype D introduction and dissemination in South Brazil. INFECTION GENETICS AND EVOLUTION 2020; 82:104294. [PMID: 32247034 DOI: 10.1016/j.meegid.2020.104294] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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]
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22
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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.
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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
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Cagliani R, Forni D, Sironi M. Mode and tempo of human hepatitis virus evolution. Comput Struct Biotechnol J 2019; 17:1384-1395. [PMID: 31768229 PMCID: PMC6872792 DOI: 10.1016/j.csbj.2019.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 02/07/2023] Open
Abstract
Human viral hepatitis, a major cause of morbidity and mortality worldwide, is caused by highly diverse viruses with different genetic, ecological, and pathogenetic features. Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. Thus, with the exclusion of hepatitis D virus, close or distant relatives of these human pathogens were identified in a number of domestic and wild mammals. Also, sequences of human viral strains isolated from different geographic locations and over different time-spans have allowed the application of phylogeographic and molecular dating approaches to large viral phylogenies. In this review, we summarize the most recent insights into our understanding of the evolutionary events and ecological contexts that determined the origin and spread of human hepatitis viruses.
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Affiliation(s)
- Rachele Cagliani
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
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24
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Sumer U, Sayan M. Molecular Epidemiology of Hepatitis B Virus in Turkish Cypriot. Pol J Microbiol 2019; 68:449-456. [PMID: 31880889 PMCID: PMC7260636 DOI: 10.33073/pjm-2019-044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 12/11/2022] Open
Abstract
There is an increased demand for molecular and epidemiological information regarding Hepatitis B Virus (HBV) infection as the disease severity depends on these specifications. We have aimed to analyze nucleos(t)ide analogues (NA) resistance and typical HBsAg escape mutations with the dispersion of HBV genotype/subgenotype/HBsAg serotypes on overlapping pol/S gene regions in the Turkish population. Samples were collected in Northern Cyprus. Reverse transcriptase (rt) region between 80–250 amino acids were amplified. Typical HBsAg escape mutations were determined as HBIg escape (6.48%), vaccine escape (8.34%), HBsAg misdiagnosis (9.25%), and immune escape mutations (8.34%). NAs resistances were determined as primary (2.78%), partial (2.78%), and compensatory mutations (26.85%) in overlapping pol/S gene region. The study patients were predominantly infected with HBV genotype D/D1 (98%). However, the predominant HBsAg serotype was ayw2 (99%). The most common NA resistance mutation was rtQ215H/P/S (16.67%), however, for S gene the misdiagnosis mutations were observed most frequently (9.25%). We can conclude that HBV D/D1 is the dominant strain and ayw2 is the dominant serotype in the Turkish Cypriot. Cyprus is an island located in the Eastern Mediterranean region, and it is, therefore, a key location for human trafficking and immigration; as a result of this reputation, it is necessary to analyze HBV phylogenetically for local dynamics, and our results indicate that treatment naïve population is prone to these pol/S gene mutations. However, if HBV strains were also analyzed among Greek Cypriots too, this would enable a complete island survey. With this work, we believe that we have enlightened this subject for further research.
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Affiliation(s)
- Unal Sumer
- Near East University, Faculty of Medicine, Department of Medical Microbiology , Nicosia , Northern Cyprus
| | - Murat Sayan
- Kocaeli University, Faculty of Medicine, Clinical Laboratory, PCR Unit , Kocaeli , Turkey ; Near East University, Research Centre of Experimental Health Sciences , Nicosia , Northern Cyprus
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25
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Sagnelli C, Sagnelli E. Towards the worldwide eradication of hepatitis B virus infection: A combination of prophylactic and therapeutic factors. World J Clin Infect Dis 2019; 9:11-22. [DOI: 10.5495/wjcid.v9.i2.11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is still a global health problem, mostly because of the intermediate/high rates of HBV chronic carriers living in most Asian, African and eastern European countries. The universal HBV vaccination of new-borns undertaken in most nations over the last 3 decades and effective HBV antiviral treatments (nucleos(t)ide analogue with high genetic barrier to viral resistance) introduced in the last decade have shown their beneficial effects in inducing a clear reduction of HBV endemicity in the countries where they have been extensively applied. Great hopes are now placed on new antiviral and immunotherapeutic drugs that are now at an advanced stage of study. It is in fact already conceivable that the synergistic use of new drugs targeting more than one HBV-lifecycle steps (covalent closed circular DNA destruction/silencing, HBV entry inhibitors, nucleocapsid assembly modulators targeting viral transcripts) and of some new immunotherapeutic agents might eliminate the intrahepatic covalent closed circular DNA and achieve the eradication of HBV infection. In spite of this, a strong effort should be given to extensive educational and screening programs for the at-risk population and to the implementation of HBV vaccination in developing countries.
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Affiliation(s)
- Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples 80131, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples 80131, Italy
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26
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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: 1.8] [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.
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27
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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: 3.8] [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.
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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
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28
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Bahar M, Pervez MT, Ali A, Babar ME. In Silico Analysis of Hepatitis B Virus Genotype D Subgenotype D1 Circulating in Pakistan, China, and India. Evol Bioinform Online 2019; 15:1176934319861337. [PMID: 31320794 PMCID: PMC6610437 DOI: 10.1177/1176934319861337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 06/05/2019] [Indexed: 12/15/2022] Open
Abstract
The focus of this study was the computational analysis of hepatitis B virus (HBV)
genotype D subgenotype D1 in Pakistan, China, and India. In total, 54 complete
genome sequences of HBV genotype D subgenotype D1 were downloaded from National
Center for Biotechnology Information (NCBI). Of these, 6 complete genome
sequences were from Pakistan, 14 were from China, and 34 were from India.
Sequence alignment showed less than 4% divergence in these sequences. C and X
genes showed divergence of less than 3%. Comparison over the S gene showed more
than 97% similarity among the nucleotide sequences of genotype D subgenotype D1.
The identity and similarity matrix of 54 nucleotide sequences of HBV genotype D
subgenotype D1 from Pakistan, China, and India revealed more than 93% identity
and 93% similarity. Phylogenetic analysis highlighted that complete genome
isolates of HBV circulating in Pakistan had the closest evolutionary
relationship with its neighboring countries China and India. China’s (HQ833466)
and Pakistan’s (AB583680.1) isolates shared the same ancestor. Gene structure
analysis showed that “P” gene exons were the longest, about three-fourth of the
genome size, whereas gene “S” had the second longest coding regions with 2 exons
and 1 intron. However, “C” and “X” genes had 1 smallest exon. X proteins had
proven role in spreading of the HBV infection diseases. For HBx analysis, 1 X
protein sequence of HBV genotype D subgenotype D1 belonging to each country was
obtained. Homology models of the 3 X proteins generated using SWISS-MODEL
revealed GMQE (Global Model Quality Estimation) = 0.1. Global and local quality
estimate scores including Z-scores for Qualitative Model Energy
Analysis (QMEAN) C-beta, all-atom, solvation, and torsion energy scores were
similar indicating good quality, accuracy, and reliability of the predicted
models. Three-dimensional (3D) visualization showed similar structures and
Ramachandran plots showed a high percentage of protein residues into the
favorable region for X protein models.
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Affiliation(s)
- Muneeb Bahar
- Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan
| | - Muhammad Tariq Pervez
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Akhtar Ali
- Department of Biotechnology, Virtual University of Pakistan, Lahore, Pakistan
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29
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Rasche A, Sander AL, Corman VM, Drexler JF. Evolutionary biology of human hepatitis viruses. J Hepatol 2019; 70:501-520. [PMID: 30472320 PMCID: PMC7114834 DOI: 10.1016/j.jhep.2018.11.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/09/2018] [Accepted: 11/10/2018] [Indexed: 02/06/2023]
Abstract
Hepatitis viruses are major threats to human health. During the last decade, highly diverse viruses related to human hepatitis viruses were found in animals other than primates. Herein, we describe both surprising conservation and striking differences of the unique biological properties and infection patterns of human hepatitis viruses and their animal homologues, including transmission routes, liver tropism, oncogenesis, chronicity, pathogenesis and envelopment. We discuss the potential for translation of newly discovered hepatitis viruses into preclinical animal models for drug testing, studies on pathogenesis and vaccine development. Finally, we re-evaluate the evolutionary origins of human hepatitis viruses and discuss the past and present zoonotic potential of their animal homologues.
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Affiliation(s)
- Andrea Rasche
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany,German Center for Infection Research (DZIF), Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - Victor Max Corman
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany,German Center for Infection Research (DZIF), Germany
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany; German Center for Infection Research (DZIF), Germany.
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30
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Caballero A, Tabernero D, Buti M, Rodriguez-Frias F. Hepatitis B virus: The challenge of an ancient virus with multiple faces and a remarkable replication strategy. Antiviral Res 2018; 158:34-44. [PMID: 30059722 DOI: 10.1016/j.antiviral.2018.07.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 02/07/2023]
Abstract
The hepatitis B virus (HBV) is the prototype member of the Hepadnaviridae, an ancient family of hepatotropic DNA viruses, which may have originated from 360 to 430 million years ago and with evidence of endogenization in reptilian genomes >200 million years ago. The virus is currently estimated to infect more than 250 million humans. The extremely successful spread of this pathogen among the human population is explained by its multiple particulate forms, effective transmission strategies (particularly perinatal transmission), long induction period and low associated mortality. These characteristics confer selective advantages, enabling the virus to persist in small, disperse populations and spread worldwide, with high prevalence rates in many countries. The HBV replication strategy is remarkably complex and includes a multiplicity of particulate structures. In addition to the common virions containing DNA in a relaxed circular (rcDNA) or double-stranded linear (dslDNA) forms, the viral population includes virion-like particles containing RNA or "empty" (viral envelopes and capsids without genomes), subviral particles (only an envelope) and even naked capsids. Consequently, several forms of the genome coexist in a single infection: (i) the "traveler" forms found in serum, including rcDNA and dslDNA, which originate from retrotranscription of a messenger RNA (the pregenomic RNA, another form of the viral genome itself) and (ii) forms confined to the host cell nucleus, including covalently closed circular DNA (cccDNA), which leads to a minichromosome form associated with histones and viral proteins, and double-stranded DNA integrated into the host genome. This complex composition lends HBV a kind of "multiple personality". Are these additional particles and genomic forms simple intermediaries/artifacts or do they play a role in the viral life cycle?
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Affiliation(s)
- Andrea Caballero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain.
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain.
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain; Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, General Hospital, Internal Medicine 2, 08035 Barcelona, Spain.
| | - Francisco Rodriguez-Frias
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona (UAB), 119-129 Passeig Vall d'Hebron, Clinical Laboratories, 08035 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 3-5 Avenida Monforte de Lemos, pavilion 11, 28029 Madrid, Spain.
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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: 3.4] [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.
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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
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Paoli JD, Wortmann AC, Klein MG, Pereira VRZB, Cirolini AM, Godoy BAD, Fagundes NJR, Wolf JM, Lunge VR, Simon D. HBV epidemiology and genetic diversity in an area of high prevalence of hepatitis B in southern Brazil. Braz J Infect Dis 2018; 22:294-304. [PMID: 30092176 PMCID: PMC9427806 DOI: 10.1016/j.bjid.2018.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/19/2018] [Accepted: 06/22/2018] [Indexed: 02/07/2023] Open
Abstract
Background Hepatitis B virus (HBV) infection is a major public health problem in Brazil. HBV endemicity is usually moderate to low according to geographic regions, and high prevalence of this virus has been reported in people of some specific Brazilian counties, including those with a strong influence of Italian colonization in southern Brazil. Analysis of HBV diversity and identification of the main risk factors to HBV infection are necessary to understand hepatitis B epidemiology in these high prevalence regions in southern Brazil. Objective To investigate epidemiological characteristics and HBV genotypes and subgenotypes circulating in a specific city with high HBV prevalence. Methods A cross-sectional study was performed with 102 HBV chronically infected individuals, recruited in reference outpatient clinics for viral hepatitis in a city of high HBV prevalence (Bento Gonçalves) in Rio Grande do Sul state, Brazil between July and December 2010. Socio-demographic, clinical and behavior-related variables were collected in a structured questionnaire. HBV serological markers (HBsAg, anti-HBc), viral load, genotypes/subgenotypes and drug resistance were evaluated and comparatively analyzed among all patients. Results The HBV infected subjects had a mean age of 44.9 (±12.2) years, with 86 patients (84.3%) reporting to have a family history of HBV infection, 51 (50.0%) to share personal objects, and were predominantly of Italian descendants (61; 64.9%). There was a predominance of genotype D (49/54; 90.7%), but genotype A was also detected (5/54; 9.3%). Subgenotypes D1 (1; 4.7%), D2 (3; 14.3%), and D3 (17; 81.0%) were identified. LAM-resistant mutation (rtM204I) and ADV-resistant mutations (rtA181V) were detected in only one patient each. Conclusions These results demonstrate a pivotal role of intrafamilial transmission for HBV spreading in this population. Furthermore, there is a high prevalence of HBV genotype D in this region.
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Affiliation(s)
- Juliana de Paoli
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brazil
| | - André Castagna Wortmann
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências em Gastroenterologia e Hepatologia, Porto Alegre, RS, Brazil
| | - Mirelli Gabardo Klein
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brazil
| | | | - Adriana Maria Cirolini
- Secretaria Municipal de Saúde de Bento Gonçalves, Serviço de Atendimento Especializado, Bento Gonçalves, RS, Brazil
| | - Bibiane Armiliato de Godoy
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Nelson Jurandi Rosa Fagundes
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Jonas Michel Wolf
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brazil.
| | - Vagner Ricardo Lunge
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brazil
| | - Daniel Simon
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brazil
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33
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Sagnelli C, Ciccozzi M, Alessio L, Cella E, Gualdieri L, Pisaturo M, Minichini C, Di Caprio G, Starace M, Onorato L, Capoprese M, Occhiello L, Angeletti S, Scotto G, Macera M, Sagnelli E, Coppola N. HBV molecular epidemiology and clinical condition of immigrants living in Italy. Infection 2018; 46:523-531. [PMID: 29796738 DOI: 10.1007/s15010-018-1153-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 05/17/2018] [Indexed: 12/13/2022]
Abstract
INTRODUCTION We investigated 170 HBsAg-positive immigrants living in Italy for 1-7 years to ascertain whether they may have become infected in the host country. METHODS Of 2032 adult immigrants interviewed, 1727 (85%) voluntarily adhered to a screening program for bloodborne or sexually transmitted infections. HBsAg was detected in 170 (9.8%) screened immigrants who completed the diagnostic, clinical and therapeutic process at the nearest clinic of infectious diseases. HBV molecular biology was performed applying a homemade technology. Phylogenetic signal of the datasets was obtained by a likelihood-mapping analysis using TreePuzzle. RESULTS Of the 170 HBsAg-positive immigrants, 133 were inactive carriers, 29 had chronic hepatitis and 8 compensated cirrhosis. HBV genotype was identified in 109 of the 113 HBV-DNA-positive immigrants and HBV-genotype-E predominated (68.9%). Of these 109, 6 (5.5%) subjects showed an HBV genotype absent or extremely rare in their native country: HBV-genotype-E in three from Eastern Europe and in one from Sri Lanka, possibly acquired from other immigrants from sub-Saharan countries, HBV-genotype-D1 in one from Burkina Faso and one from Senegal, possibly acquired in Italy. CONCLUSION The data suggest that immigrants may acquire HBV infection in Italy and, therefore, HBV vaccination programs should be extended to all immigrants living in Italy.
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Affiliation(s)
- Caterina Sagnelli
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy.,Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy.,Medical Center, Centro Suore Missionarie della Carità, Naples, Italy
| | - Massimo Ciccozzi
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Loredana Alessio
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Eleonora Cella
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Luciano Gualdieri
- Medical Center, Centro per la Tutela della Salute degli Immigrati, Naples, Italy
| | - Mariantonietta Pisaturo
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy.,Infectious Diseases Unit, AORN Sant'Anna e San Sebastiano, Caserta, Italy
| | - Carmine Minichini
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy
| | - Giovanni Di Caprio
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Mario Starace
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy
| | - Lorenzo Onorato
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Mara Capoprese
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Laura Occhiello
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | | | - Margherita Macera
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy.,Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Medical Center, Centro di Accoglienza "La tenda di Abramo", Caserta, Italy
| | - Evangelista Sagnelli
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy.
| | - Nicola Coppola
- Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy
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34
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Mühlemann B, Jones TC, Damgaard PDB, Allentoft ME, Shevnina I, Logvin A, Usmanova E, Panyushkina IP, Boldgiv B, Bazartseren T, Tashbaeva K, Merz V, Lau N, Smrčka V, Voyakin D, Kitov E, Epimakhov A, Pokutta D, Vicze M, Price TD, Moiseyev V, Hansen AJ, Orlando L, Rasmussen S, Sikora M, Vinner L, Osterhaus ADME, Smith DJ, Glebe D, Fouchier RAM, Drosten C, Sjögren KG, Kristiansen K, Willerslev E. Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature 2018; 557:418-423. [PMID: 29743673 DOI: 10.1038/s41586-018-0097-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 04/06/2018] [Indexed: 12/16/2022]
Abstract
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
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Affiliation(s)
- Barbara Mühlemann
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Terry C Jones
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.,Institute of Virology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Irina Shevnina
- Archaeological Laboratory, Faculty of History and Law, A. A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Andrey Logvin
- Archaeological Laboratory, Faculty of History and Law, A. A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Emma Usmanova
- Saryarka Archaeological Institute, Karaganda State University, Karaganda, Kazakhstan
| | | | - Bazartseren Boldgiv
- Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tsevel Bazartseren
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia
| | | | - Victor Merz
- Pavlodar State University, Pavlodar, Kazakhstan
| | - Nina Lau
- Centre for Baltic and Scandinavian Archaeology, Schleswig, Germany
| | - Václav Smrčka
- Institute for History of Medicine and Foreign Languages of the First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Egor Kitov
- N. N. Miklouho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Epimakhov
- South Ural Department, Institute of History and Archaeology UBRAS, South Ural State University, Chelyabinsk, Russia
| | - Dalia Pokutta
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - T Douglas Price
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Vyacheslav Moiseyev
- Department of Physical Anthropology, Peter the Great Museum of Anthropology and Ethnography, Saint-Petersburg, Russia
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Dieter Glebe
- Institute of Medical Virology, Justus Liebig University of Giessen, Giessen, Germany.,National Reference Centre for Hepatitis B and D Viruses, German Center for Infection Research (DZIF), Giessen, Germany
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Christian Drosten
- Institute of Virology, Charité, Universitätsmedizin Berlin, Berlin, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | | | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. .,Cambridge GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Trust Sanger Institute, Hinxton, UK.
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35
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Fragoso-Fonseca DE, Escobar-Escamilla N, Lloret Y Sánchez LT, Wong-Arámbula CE, Hernández-Rivas L, Díaz-Quiñonez JA, Ramírez-González JE. Full genome and phylogenetic analysis of hepatitis B virus genotype F in Mexican isolates. Arch Virol 2018; 163:1981-1984. [PMID: 29549442 DOI: 10.1007/s00705-018-3813-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/08/2018] [Indexed: 12/14/2022]
Abstract
Hepatitis B virus genotype F (HBV/F) is endemic in Central and South America with a minor proportion in Mexico and North America. HBV/F is divided into subgenotypes and subtypes with particular geographic circulation patterns. Here, we report the complete genome sequence and molecular characterization of HBV/F from three isolates. Phylogenetic analysis with all available HBV/F sequences showed that our sequences belonged to the F1b subtype and, in addition, the absence of the previously reported F1a subtype in Mexican isolates. Our findings suggest the circulation of HBV/F1b, the first phylogenomic study of HBV/F in Mexico.
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Affiliation(s)
- David Esaú Fragoso-Fonseca
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Álvaro Obregón, Mexico City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, S/N, Casco de Santo Tomás, 11340, Miguel Hidalgo, Mexico City, Mexico
| | - Noé Escobar-Escamilla
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Álvaro Obregón, Mexico City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, S/N, Casco de Santo Tomás, 11340, Miguel Hidalgo, Mexico City, Mexico
| | - Lourdes Teresa Lloret Y Sánchez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Álvaro Obregón, Mexico City, Mexico
| | - Claudia Elena Wong-Arámbula
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Álvaro Obregón, Mexico City, Mexico
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Álvaro Obregón, Mexico City, Mexico
| | - José Alberto Díaz-Quiñonez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Álvaro Obregón, Mexico City, Mexico
- División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Paseo de las Facultades S/N, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - José Ernesto Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Álvaro Obregón, Mexico City, Mexico.
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36
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de Pina-Araujo IIM, Spitz N, Soares CC, Niel C, Lago BV, Gomes SA. Hepatitis B virus genotypes A1, A2 and E in Cape Verde: Unequal distribution through the islands and association with human flows. PLoS One 2018; 13:e0192595. [PMID: 29447232 PMCID: PMC5813952 DOI: 10.1371/journal.pone.0192595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/28/2018] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) diversity has not been previously studied in Cape Verde. The archipelago was discovered in 1460 by Portuguese explorers, who brought African slaves to colonise the islands. In this study, we investigated the HBV characteristics from 183 HBsAg-positive Cape Verdean individuals. Phylogenetic analysis of the pre-S/S region and the full-length genomes revealed 54 isolates with HBV/A1 (57%), 21 with HBV/A2 (22%), 19 with HBV/E (20%), and one with HBV/D (1%). HBV genotypes and subgenotypes were unequally distributed through the islands. In São Vicente, the main northern island, most isolates (84%) belonged to the African-originated HBV/A1, with the remaining isolates belonging to HBV/A2, which is prevalent in Europe. Interestingly, the HBV/A1 isolates from São Vicente were closely related to Brazilian sequences into the Asian-American clade, which suggests the dissemination of common African ancestors through slave trade. In contrast, in Santiago and nearby southern islands, where a recent influx from different populations circulates, a higher diversity of HBV was observed: HBV/A1 (40%); HBV/E (32%); HBV/A2 (28%); and HBV/D (1%). HBV/E is a recent genotype disseminated in Africa that was absent in the era of the slave trade. African and European human flows at different times of the history may explain the HBV diversity in Cape Verde. The possible origin and specifics of each HBV genotype circulating in Cape Verde are discussed.
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Affiliation(s)
| | - Natalia Spitz
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Caroline C. Soares
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Christian Niel
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Barbara V. Lago
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), FIOCRUZ, Rio de Janeiro, Brazil
| | - Selma A. Gomes
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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37
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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: 1.7] [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.
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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
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38
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Li M, Chen L, Liu LM, Li YL, Li BA, Li B, Mao YL, Xia LF, Wang T, Liu YN, Li Z, Guo TS. Performance verification and comparison of TianLong automatic hypersensitive hepatitis B virus DNA quantification system with Roche CAP/CTM system. World J Gastroenterol 2017; 23:6845-6853. [PMID: 29085227 PMCID: PMC5645617 DOI: 10.3748/wjg.v23.i37.6845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/01/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023] Open
Abstract
AIM To investigate and compare the analytical and clinical performance of TianLong automatic hypersensitive hepatitis B virus (HBV) DNA quantification system and Roche CAP/CTM system.
METHODS Two hundred blood samples for HBV DNA testing, HBV-DNA negative samples and high-titer HBV-DNA mixture samples were collected and prepared. National standard materials for serum HBV and a worldwide HBV DNA panel were employed for performance verification. The analytical performance, such as limit of detection, limit of quantification, accuracy, precision, reproducibility, linearity, genotype coverage and cross-contamination, was determined using the TianLong automatic hypersensitive HBV DNA quantification system (TL system). Correlation and Bland-Altman plot analyses were carried out to compare the clinical performance of the TL system assay and the CAP/CTM system.
RESULTS The detection limit of the TL system was 10 IU/mL, and its limit of quantification was 30 IU/mL. The differences between the expected and tested concentrations of the national standards were less than ± 0.4 Log10 IU/mL, which showed high accuracy of the system. Results of the precision, reproducibility and linearity tests showed that the multiple test coefficient of variation (CV) of the same sample was less than 5% for 102-106 IU/mL; and for 30-108 IU/mL, the linear correlation coefficient r2 = 0.99. The TL system detected HBV DNA (A-H) genotypes and there was no cross-contamination during the “checkerboard” test. When compared with the CAP/CTM assay, the two assays showed 100% consistency in both negative and positive sample results (15 negative samples and 185 positive samples). No statistical differences between the two assays in the HBV DNA quantification values were observed (P > 0.05). Correlation analysis indicated a significant correlation between the two assays, r2 = 0.9774. The Bland-Altman plot analysis showed that 98.9% of the positive data were within the 95% acceptable range, and the maximum difference was -0.49.
CONCLUSION The TL system has good analytical performance, and exhibits good agreement with the CAP/CTM system in clinical performance.
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Affiliation(s)
- Ming Li
- School of Mechanical Engineering, Xi’an Jiaotong University. Xi’an 710049, Shaanxi Province, China
- Xi’an TianLong Science and Technology Co., Ltd., Xi’an 710018, Shaanxi Province, China
| | - Lin Chen
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
| | - Li-Ming Liu
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Yong-Li Li
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
| | - Bo-An Li
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
| | - Bo Li
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
| | - Yuan-Li Mao
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
| | - Li-Fang Xia
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
| | - Tong Wang
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
| | - Ya-Nan Liu
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
| | - Zheng Li
- Xi’an TianLong Science and Technology Co., Ltd., Xi’an 710018, Shaanxi Province, China
| | - Tong-Sheng Guo
- Center of Clinical Laboratory Medicine, 302 Military Hospital of China, Beijing 100039, China
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Cavaretto L, Motta-Castro ARC, Teles SA, Souza FQ, Cardoso WM, de Rezende GR, Tanaka TSO, Bandeira LM, Cesar GA, Puga MAM, Nepomuceno BB, Lago BV, Fernandes-Fitts SM. Epidemiological and molecular analysis of hepatitis B virus infection in manicurists in Central Brazil. J Med Virol 2017; 90:277-281. [PMID: 28885693 DOI: 10.1002/jmv.24940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/24/2017] [Indexed: 12/14/2022]
Abstract
The aim of this study was to investigate the serological and molecular prevalence of hepatitis B virus (HBV) infection in 514 manicurists/pedicurists and identify the risk factors related with this infection. Samples were tested for HBV serological markers, hepatitis C virus (HCV), and human immunodeficiency virus (HIV) by enzyme-linked immunosorbent assay (ELISA). Anti-HBc-positive samples were tested to investigate occult hepatitis B by PCR. HBsAg-positive samples were genotyped and the viral loads of HBV-DNA positive samples were quantified. The overall HBV prevalence was 5.6% (29/514) and of HBsAg was 0.4% (2/514). One case of occult hepatitis B was found. The genotypes A1 and F2 were identified in two HBsAg-positive samples. Low level of education, not being born in the State of Mato Grosso do Sul and working in the central region of the city were associated with the HBV infection. No single manicurist/pedicurist was infected by HCV or HIV. These findings suggest that despite the exposure to blood contact, this occupation was not associated to an increased risk of acquiring HBV, HCV, and HIV infections.
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Affiliation(s)
- Larissa Cavaretto
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Ana R C Motta-Castro
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.,Fundação Oswaldo Cruz, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Fernanda Q Souza
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Wesley M Cardoso
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Tayana S O Tanaka
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Larissa M Bandeira
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Gabriela A Cesar
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Marco A M Puga
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Bruna B Nepomuceno
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Bárbara V Lago
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Instituto de Tecnologia em Imunobiológicos-Biomanguinhos, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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40
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Hepatitis B Virus Genotypes, Epidemiological Characteristics and Clinical Presentation of HBV Chronic Infection in Immigrant Populations Living in Southern Italy. HEPATITIS MONTHLY 2017. [DOI: 10.5812/hepatmon.13740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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41
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Lauber C, Seitz S, Mattei S, Suh A, Beck J, Herstein J, Börold J, Salzburger W, Kaderali L, Briggs JAG, Bartenschlager R. Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses. Cell Host Microbe 2017; 22:387-399.e6. [PMID: 28867387 PMCID: PMC5604429 DOI: 10.1016/j.chom.2017.07.019] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/10/2017] [Accepted: 07/29/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome organization with extensive gene overlap. Remarkably, the ∼1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of HBVs including genome replication via protein-primed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction indicates that these two virus families separated more than 400 million years ago before the rise of tetrapods. We show that HBVs are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo, leading to a major transition in viral lifestyle, followed by co-evolution with their hosts over geologic eras.
Nackednaviruses are non-enveloped fish viruses related to hepadnaviruses Both virus families separated from a common ancestor >400 million years ago The envelope protein gene of hepadnaviruses emerged through two distinct processes Hepadnaviruses mainly co-evolve with hosts while nackednaviruses jump between hosts
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Affiliation(s)
- Chris Lauber
- Institute for Medical Informatics and Biometry, Technische Universität Dresden, 01307 Dresden, Germany
| | - Stefan Seitz
- University of Heidelberg, Department of Infectious Diseases, Molecular Virology, 69120 Heidelberg, Germany.
| | - Simone Mattei
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, 75236 Uppsala, Sweden
| | - Jürgen Beck
- Department of Internal Medicine 2/Molecular Biology, University Hospital Freiburg, 79106 Freiburg, Germany
| | - Jennifer Herstein
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jacob Börold
- University of Heidelberg, Department of Infectious Diseases, Molecular Virology, 69120 Heidelberg, Germany
| | | | - Lars Kaderali
- Institute for Medical Informatics and Biometry, Technische Universität Dresden, 01307 Dresden, Germany; Institute for Bioinformatics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ralf Bartenschlager
- University of Heidelberg, Department of Infectious Diseases, Molecular Virology, 69120 Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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42
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Bouckaert R, Simons BC, Krarup H, Friesen TM, Osiowy C. Tracing hepatitis B virus (HBV) genotype B5 (formerly B6) evolutionary history in the circumpolar Arctic through phylogeographic modelling. PeerJ 2017; 5:e3757. [PMID: 28875087 PMCID: PMC5581946 DOI: 10.7717/peerj.3757] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/12/2017] [Indexed: 12/11/2022] Open
Abstract
Background Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence) with hepatitis B virus (HBV), with subgenotype B5 (formerly B6) unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association. Methods To investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2) using a reversible-jump-based substitution model and a clock rate estimated at 4.1 × 10−5 substitutions/site/year. Results Following an initial divergence from an Asian viral ancestor approximately 1954 years before present (YBP; 95% highest probability density interval [1188, 2901]), HBV/B5 coalescence occurred almost 1000 years later. Surprisingly, the HBV/B5 ancestor appears to locate first to Greenland in a rapid coastal route progression based on the landscape aware geographic model, with subsequent B5 evolution and spread westward. Bayesian skyline plot analysis demonstrated an HBV/B5 population expansion occurring approximately 400 YBP, coinciding with the disruption of the Neo-Eskimo Thule culture into more heterogeneous and regionally distinct Inuit populations throughout the North American Arctic. Discussion HBV/B5 origin and spread appears to occur coincident with the movement of Neo-Eskimo (Inuit) populations within the past 1000 years, further supporting the hypothesis of HBV/host co-expansion, and illustrating the concept of host-pathogen adaptation and balance.
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Affiliation(s)
- Remco Bouckaert
- Department of Computer Science, University of Auckland, Auckland, New Zealand
| | - Brenna C Simons
- Alaska Native Tribal Health Consortium, Anchorage, AK, United States of America
| | - Henrik Krarup
- Section of Molecular Diagnostics, Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - T Max Friesen
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Carla Osiowy
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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43
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Sagnelli E, Alessio L, Sagnelli C, Gualdieri L, Pisaturo M, Minichini C, Di Caprio G, Starace M, Onorato L, Macera M, Scotto G, Coppola N. Hepatitis B Virus Genotypes, Epidemiological Characteristics, and Clinical Presentation of HBV Chronic Infection in Immigrant Populations Living in Southern Italy. HEPATITIS MONTHLY 2017; 17. [DOI: 10.5812/hepatmon.13260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2025]
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44
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Lawson-Ananissoh LM, Attia KA, Diallo D, Doffou S, Kissi YH, Bangoura D, Kouamé D, Mahassadi KA, Yao-Bathaix F, Yoman TN. Distribution et implications cliniques des génotypes du virus de l’hépatite B chez 33 porteurs chroniques du virus de l’hépatite B en Côte-d’Ivoire. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s12157-017-0726-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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45
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Li S, Wang Z, Li Y, Ding G. Adaptive evolution of proteins in hepatitis B virus during divergence of genotypes. Sci Rep 2017; 7:1990. [PMID: 28512348 PMCID: PMC5434055 DOI: 10.1038/s41598-017-02012-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/03/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B virus (HBV) is classified into several genotypes, correlated with different geographic distributions, clinical outcomes and susceptible human populations. It is crucial to investigate the evolutionary significance behind the diversification of HBV genotypes, because it improves our understanding of their pathological differences and pathogen-host interactions. Here, we performed comprehensive analysis of HBV genome sequences collected from public database. With a stringent criteria, we generated a dataset of 2992 HBV genomes from eight major genotypes. In particular, we applied a specified classification of non-synonymous and synonymous variants in overlapping regions, to distinguish joint and independent gene evolutions. We confirmed the presence of selective constraints over non-synonymous variants in consideration of overlapping regions. We then performed the McDonald-Kreitman test and revealed adaptive evolutions of non-synonymous variants during genotypic differentiation. Remarkably, we identified strong positive selection that drove the differentiation of PreS1 domain, which is an essential regulator involved in viral transmission. Our study presents novel evidences for the adaptive evolution of HBV genotypes, which suggests that these viruses evolve directionally for maintenance or improvement of successful infections.
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Affiliation(s)
- Shengdi Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Zhen Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China.
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, 1278 Keyuan Road, 201203, Shanghai, China.
| | - Guohui Ding
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China.
- Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, 1278 Keyuan Road, 201203, Shanghai, China.
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46
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Lo Presti A, Andriamandimby SF, Lai A, Angeletti S, Cella E, Mottini G, Guarino MPL, Balotta C, Galli M, Heraud JM, Zehender G, Ciccozzi M. Origin and evolutionary dynamics of Hepatitis B virus (HBV) genotype E in Madagascar. Pathog Glob Health 2017; 111:23-30. [PMID: 28081689 DOI: 10.1080/20477724.2016.1278103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Africa is one of the endemic regions of HBV infection. In particular, genotype E is highly endemic in most of sub-Saharan Africa such as West African countries where it represents more than 90% of total infections. Madagascar, which is classified as a high endemic area for HBV and where the most prevalent genotype is E, might play a relevant role in the dispersion of this genotype due to its crucial position in the Indian Ocean. The aim of this study was to investigate the origin, population dynamics, and circulation of HBV-E genotype in Madagascar through high-resolution phylogenetic and phylodynamic approaches. The phylogenetic tree indicated that Malagasy isolates were intermixed and closely related with sequences mostly from West African countries. The Bayesian tree highlighted three statistically supported clusters of Malagasy strains which dated back to the years 1981 (95% HPD: 1971-1992), 1986 (95% HPD: 1974-1996), and 1989 (95% HPD: 1974-2001). Population dynamics analysis showed an exponential increase in the number of HBV-E infections approximately from the year 1975 until 2000s. The migration analysis was also performed and a dynamic pattern of gene flow was identified. In conclusion, this study confirms previous observation of HBV-E circulation in Africa and expands these findings at Madagascar demonstrating its recent introduction, and highlighting the role of the African countries in the spread of HBV-E genotype. Further studies on molecular epidemiology of HBV genotype E are needed to clarify the evolutionary history of this genotype.
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Affiliation(s)
- Alessandra Lo Presti
- a Epidemiology Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases , Istituto Superiore di Sanità , Rome , Italy
| | | | - Alessia Lai
- c Department of Biomedical and Clinical Sciences "Luigi Sacco", Infectious Diseases and Immunopathology Section, 'L. Sacco' Hospital , University of Milan , Milan , Italy
| | - Silvia Angeletti
- d Clinical Pathology and Microbiology Laboratory , University Hospital Campus Bio-Medico of Rome , Rome , Italy
| | - Eleonora Cella
- a Epidemiology Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases , Istituto Superiore di Sanità , Rome , Italy.,e Public Health and Infectious Diseases , Sapienza University , Rome , Italy
| | | | | | - Claudia Balotta
- c Department of Biomedical and Clinical Sciences "Luigi Sacco", Infectious Diseases and Immunopathology Section, 'L. Sacco' Hospital , University of Milan , Milan , Italy
| | - Massimo Galli
- c Department of Biomedical and Clinical Sciences "Luigi Sacco", Infectious Diseases and Immunopathology Section, 'L. Sacco' Hospital , University of Milan , Milan , Italy
| | - Jean-Michel Heraud
- b Virology Unit , Institut Pasteur of Madagascar , Antananarivo , Madagascar
| | - Gianguglielmo Zehender
- c Department of Biomedical and Clinical Sciences "Luigi Sacco", Infectious Diseases and Immunopathology Section, 'L. Sacco' Hospital , University of Milan , Milan , Italy
| | - Massimo Ciccozzi
- a Epidemiology Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases , Istituto Superiore di Sanità , Rome , Italy.,f University Hospital Campus Bio-Medico , Rome , Italy
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47
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Sagnelli C, Ciccozzi M, Coppola N, Minichini C, Lo Presti A, Starace M, Alessio L, Macera M, Cella E, Gualdieri L, Caprio N, Pasquale G, Sagnelli E. Molecular diversity in irregular or refugee immigrant patients with HBV-genotype-E infection living in the metropolitan area of Naples. J Med Virol 2016; 89:1015-1024. [PMID: 27805272 DOI: 10.1002/jmv.24724] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2016] [Indexed: 12/12/2022]
Abstract
In a recent testing in the metropolitan area of Naples, Italy, on 945 irregular immigrants or refugees, 87 HBsAg chronic carriers were identified, 53 of whom were infected by HBV-genotype E. The aim of the present study was to identify the genetic diversity of HBV-genotype E in these 53 immigrants. The 53 immigrant patients with HBV-genotype-E infection were born in Africa, central or eastern Asia, eastern Europe or Latin America. These patients had been seen for a clinical consultation at one of the four first-level units from January 2012 to 2013. The first dataset contained 53 HBV-S gene isolates plus 128 genotype/subgenotype specific reference sequences downloaded from the National Center for Biotechnology Information. The second dataset, comprising the 53 HBV-S gene isolates, previously classified as HBV-genotype E, was used to perform the time-scaled phylogeny reconstruction using a Bayesian approach. Phylogenetic analysis showed that all 53 HBV-S isolates belonged to HBV-genotype E. Bayes factor analysis showed that the relaxed clock exponential growth model fitted the data significantly better than the other models. The time-scaled Bayesian phylogenetic tree of the second dataset showed that the root of the tree dated back to the year 1990 (95% HPD:1984-2000). Four statistically supported clusters were identified. Cluster A dated back to 2012 (95% HPD:1997-2012); cluster B dated back to 2008 (95% HPD:2001-2015); cluster C to 2006 (95% HPD:1999-2013); cluster D to 2004 (95% HPD:1998-2011). This study disclosed the genetic evolution and phylogenesis in a group of HBV-genotype-E-infected immigrants. J. Med. Virol. 89:1015-1024, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Caterina Sagnelli
- Department of Clinical and Experimental Medicine and Surgery, Second University of Naples, Naples, Italy.,Medical Center, Centro Sociale ex Canapificio, Caserta, Italy
| | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy.,University of Biomedical Campus, Rome, Italy
| | - Nicola Coppola
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Carmine Minichini
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Alessandra Lo Presti
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Mario Starace
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Loredana Alessio
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Margherita Macera
- Medical Center, Centro Sociale ex Canapificio, Caserta, Italy.,Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Eleonora Cella
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy.,Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Luciano Gualdieri
- Medical Center, Centro per la Tutela della Salute degli Immigrati, Naples, Italy
| | - Nunzio Caprio
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy.,Medical center, Centro Suore Missionarie della Carità, Naples, Italy
| | - Giuseppe Pasquale
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Second University of Naples, Naples, Italy
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Thurnheer MC, Edwards R, Schulz TR, Yuen L, Littlejohn M, Revill P, Bannister E, Chu M, Tanyeri F, Wade A, Biggs BA, Sasadeusz J. Genotypic profiles of hepatitis B in African immigrants and their clinical relevance. J Med Virol 2016; 89:1000-1007. [PMID: 27862013 DOI: 10.1002/jmv.24732] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 01/05/2023]
Abstract
Hepatitis B virus (HBV) from 40 adult African immigrants in Australia was characterized to determine the prevalence of different HBV genotypes and subgenotypes. A mutational analysis was then performed to determine the presence of clinically significant mutations and correlate them to clinical outcomes. Initial sequencing analysis revealed 13 with genotype A (32.5%), 13 with genotype D (32.5%), and 14 with genotype E (35%). Serology showed that 37 were HBeAg negative. Phylogenetic analysis identified a high prevalence (25%) of HBV subgenotype A1 in our cohort, a subgenotype which has been associated with more aggressive clinical disease. BCP/PC sequencing was obtained for 38 patients. BCP and/or PC mutations were identified in 36/38 (95%). The median viral load of all patients was 2995 IU/mL and most of the pathology results were within the normal range. Only one patient had an increased APRI score of 1.1 suggestive of cirrhosis. We present novel information on the HBV genotypes amongst the African population in Australia along with clinical correlates. The high prevalence of A1 subgenotype in this population supports the current Australian recommendation to commence hepatocellular carcinoma screening in Africans with chronic HBV from 20 years old.
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Affiliation(s)
- Maria Christine Thurnheer
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
| | - Rosalind Edwards
- Victorian Infectious Diseases Reference Laboratory, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
| | - Thomas Ray Schulz
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Victoria, 3000, Australia.,Department of Medicine/ RMH, University of Melbourne, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
| | - Lilly Yuen
- Victorian Infectious Diseases Reference Laboratory, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
| | - Peter Revill
- Victorian Infectious Diseases Reference Laboratory, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
| | - Elizabeth Bannister
- Victorian Infectious Diseases Reference Laboratory, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
| | - Melissa Chu
- Department of Medicine, University of Melbourne, Parkville, Victoria, 3050, Australia
| | - Firuz Tanyeri
- Department of Medicine, University of Melbourne, Parkville, Victoria, 3050, Australia
| | - Amanda Wade
- Department of Infectious Diseases, University Hospital, Geelong, Victoria, 3220, Australia
| | - Beverley-Ann Biggs
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Victoria, 3000, Australia.,Department of Medicine/ RMH, University of Melbourne, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
| | - Joseph Sasadeusz
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Victoria, 3000, Australia
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49
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Li X, Liu Y, Xin S, Ji D, You S, Hu J, Zhao J, Wu J, Liao H, Zhang XX, Xu D. Comparison of Detection Rate and Mutational Pattern of Drug-Resistant Mutations Between a Large Cohort of Genotype B and Genotype C Hepatitis B Virus-Infected Patients in North China. Microb Drug Resist 2016; 23:516-522. [PMID: 27792585 DOI: 10.1089/mdr.2016.0093] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The study aimed to investigate the association of prevalent genotypes in China (HBV/C and HBV/B) with HBV drug-resistant mutations. A total of 13,847 nucleos(t)ide analogue (NA)-treated patients with chronic HBV infection from North China were enrolled. HBV genotypes and resistant mutations were determined by direct sequencing and confirmed by clonal sequencing if necessary. HBV/B, HBV/C, and HBV/D occupied 14.3%, 84.9%, and 0.8% across the study population, respectively. NA usage had no significant difference between HBV/B- and HBV/C-infected patients. Lamivudine-resistant mutations were more frequently detected in HBV/C-infected patients, compared with HBV/B-infected patients (31.67% vs. 25.26%, p < 0.01). Adefovir- and entecavir-resistant mutation detection rates were similar, but the mutational pattern was different between the two genotypes. For adefovir-resistant mutations, HBV/C-infected patients had a higher detection rate of rtA181 V (HBV/C 5.29% vs. HBV/B 1.36%, p < 0.01) and a lower detection rate of rtN236T (2.70% vs. 6.54%, p < 0.01). For entecavir-resistant mutations, HBV/C-infected patients had a higher detection rate of rtM204 V/I+T184 substitution or S202G/C (3.66% vs. 2.16%, p < 0.01) and a lower detection rate of rtM204 V/I+M250 V/I/L substitution (0.67% vs. 1.46%, p < 0.01). Multidrug-resistant mutations (defined as coexistence of mutation to nucleoside and nucleotide analogues) were detected in 104 patients. HBV/C-infected patients had a higher detection rate of multidrug-resistant mutation than HBV/B-infected patients (0.83% vs. 0.35%, p < 0.05). The study for the first time clarified that HBV/C-infected patients had a higher risk to develop multidrug-resistant mutations, compared with HBV/B-infected patients; and HBV/C- and HBV/B-infected patients had different inclinations in the ETV-resistant mutational pattern.
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Affiliation(s)
- Xiaodong Li
- 1 Research Center for Clinical and Translational Medicine , Beijing 302 Hospital, Beijing, China
| | - Yan Liu
- 1 Research Center for Clinical and Translational Medicine , Beijing 302 Hospital, Beijing, China
| | - Shaojie Xin
- 2 Medical Center for Liver Failure , Beijing 302 Hospital, Beijing, China
| | - Dong Ji
- 2 Medical Center for Liver Failure , Beijing 302 Hospital, Beijing, China
| | - Shaoli You
- 2 Medical Center for Liver Failure , Beijing 302 Hospital, Beijing, China
| | - Jinhua Hu
- 2 Medical Center for Liver Failure , Beijing 302 Hospital, Beijing, China
| | - Jun Zhao
- 2 Medical Center for Liver Failure , Beijing 302 Hospital, Beijing, China
| | - Jingjing Wu
- 1 Research Center for Clinical and Translational Medicine , Beijing 302 Hospital, Beijing, China
| | - Hao Liao
- 1 Research Center for Clinical and Translational Medicine , Beijing 302 Hospital, Beijing, China
| | - Xin-Xin Zhang
- 3 Department of Infectious Diseases, Rui Jin Hospital, Shanghai Jiao Tong University , Shanghai, China
| | - Dongping Xu
- 1 Research Center for Clinical and Translational Medicine , Beijing 302 Hospital, Beijing, China
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50
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Abstract
Hepatitis B virus (HBV) infection is a major global health problems leading to severe liver disease such as cirrhosis and hepatocellular carcinoma (HCC). HBV is a circular, partly double-stranded DNA virus with various serological markers: hepatitis B surface antigen (HBsAg) and anti-HBs, anti-HBc IgM and IgG, and hepatitis B e antigen (HBeAg) and anti-HBe. It is transmitted by sexual, parenteral and vertical route. One significant method to diminish the burden of this disease is timely diagnosis of acute, chronic and occult cases of HBV. First step of HBV diagnosis is achieved by using serological markers for detecting antigens and antibodies. In order to verify first step of diagnosis, to quantify viral load and to identify genotypes, quantitative or qualitative molecular tests are used. In this article, the serological and molecular tests for diagnosis of HBV infection will be reviewed.
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Affiliation(s)
- Jeong Eun Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Do Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
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