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Li Y, Wang F, Zhou J, Li L, Song C, Chen E. Optimal Treatment Based on Interferon No Longer Makes Clinical Cure of Chronic Hepatitis B Far Away: An Evidence-Based Review on Emerging Clinical Data. Clin Pharmacol Ther 2024; 116:295-303. [PMID: 38686952 DOI: 10.1002/cpt.3287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Chronic hepatitis B (CHB) remains a major global public health problem. The functional cure is the ideal therapeutic target recommended by the latest guidelines, and pursuing a functional cure has become the key treatment end point of current therapy and for upcoming clinical trials. In this review, based on the latest published clinical research evidence, we analyzed the concept and connotation of clinical cures and elaborated on the benefits of clinical cures in detail. Secondly, we have summarized various potential treatment methods for achieving clinical cures, especially elaborating on the latest research progress of interferon-based optimized treatment strategies in achieving clinical cures. We also analyzed which populations can achieve clinical cures and conducted a detailed analysis of relevant virological and serological markers in screening clinical cure advantage populations and predicting clinical cure achievement. In addition, we also introduced the difficulties that may be encountered in the current pursuit of achieving a clinical cure.
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Affiliation(s)
- Yujing Li
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Fada Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Zhou
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Lanqing Li
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Chengrun Song
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Enqiang Chen
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
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2
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Potter BI, Thijssen M, Trovão NS, Pineda-Peña A, Reynders M, Mina T, Alvarez C, Amini-Bavil-Olyaee S, Nevens F, Maes P, Lemey P, Van Ranst M, Baele G, Pourkarim MR. Contemporary and historical human migration patterns shape hepatitis B virus diversity. Virus Evol 2024; 10:veae009. [PMID: 38361827 PMCID: PMC10868554 DOI: 10.1093/ve/veae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 10/16/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
Infection by hepatitis B virus (HBV) is responsible for approximately 296 million chronic cases of hepatitis B, and roughly 880,000 deaths annually. The global burden of HBV is distributed unevenly, largely owing to the heterogeneous geographic distribution of its subtypes, each of which demonstrates different severity and responsiveness to antiviral therapy. It is therefore crucial to the global public health response to HBV that the spatiotemporal spread of each genotype is well characterized. In this study, we describe a collection of 133 newly sequenced HBV strains from recent African immigrants upon their arrival in Belgium. We incorporate these sequences-all of which we determine to come from genotypes A, D, and E-into a large-scale phylogeographic study with genomes sampled across the globe. We focus on investigating the spatio-temporal processes shaping the evolutionary history of the three genotypes we observe. We incorporate several recently published ancient HBV genomes for genotypes A and D to aid our analysis. We show that different spatio-temporal processes underlie the A, D, and E genotypes with the former two having originated in southeastern Asia, after which they spread across the world. The HBV E genotype is estimated to have originated in Africa, after which it spread to Europe and the Americas. Our results highlight the use of phylogeographic reconstruction as a tool to understand the recent spatiotemporal dynamics of HBV, and highlight the importance of supporting vulnerable populations in accordance with the needs presented by specific HBV genotypes.
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Affiliation(s)
- Barney I Potter
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Marijn Thijssen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Nídia Sequeira Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, United States
| | - Andrea Pineda-Peña
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT; Universidade Nova de Lisboa, UNL, Portugal Rua da Junqueira No 100, Lisbon 1349-008, Portugal
- Molecular Biology and Immunology Department, Fundacion Instituto de Inmunología de Colombia (FIDIC); Faculty of Animal Science, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A.), Avenida 50 No. 26-20, Bogota 0609, Colombia
| | - Marijke Reynders
- Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Jan Brugge-Oostende AV, Ruddershove 10, Bruges B-8000, Belgium
| | - Thomas Mina
- Nonis Lab Microbiology—Virology Unit, Gregori Afxentiou 5, Limassol 4003, Cyprus
| | - Carolina Alvarez
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Samad Amini-Bavil-Olyaee
- Cellular Sciences Department, Process Virology, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospital Leuven, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Marc Van Ranst
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
| | - Mahmoud Reza Pourkarim
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Herestraat 49, Leuven BE-3000, Belgium
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion, Hemmat Exp.Way, Tehran 14665-1157, Iran
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3
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Tshiabuila D, Choga W, James SE, Maponga T, Preiser W, van Zyl G, Moir M, van Wyk S, Giandhari J, Pillay S, Anyaneji UJ, Lessells RJ, Naidoo Y, Sanko TJ, Wilkinson E, Tegally H, Baxter C, Martin DP, de Oliveira T. An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.19.24301519. [PMID: 38293032 PMCID: PMC10827254 DOI: 10.1101/2024.01.19.24301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Chronic hepatitis B virus (HBV) infection remains a significant public health concern, particularly in Africa, where there is a substantial burden. HBV is an enveloped virus, with isolates being classified into ten phylogenetically distinct genotypes (A - J) determined based on full-genome sequence data or reverse hybridization-based diagnostic tests. In practice, limitations are noted in that diagnostic sequencing, generally using Sanger sequencing, tends to focus only on the S-gene, yielding little or no information on intra-patient HBV genetic diversity with very low-frequency variants and reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV genotyping protocol suitable for clinical virology, yielding complete HBV genome sequences and extensive data on intra-patient HBV diversity. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit, ONT GridION sequencing, genotyping using Genome Detective software, recombination analysis using jpHMM and RDP5 software, and drug resistance profiling using Geno2pheno software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 left-over diagnostic Hepatitis B patient samples obtained in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.
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Affiliation(s)
- Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Wonderful Choga
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - San E. James
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Stephanie van Wyk
- Collaborating Centre for Optimizing Antimalarial Therapy (CCOAT), Mitigating Antimalarial Resistance Consortium in South East Africa (MARC SEA), Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, South Africa
| | - Jennifer Giandhari
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Richard J. Lessells
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
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Toyé RM, Loureiro CL, Jaspe RC, Zoulim F, Pujol FH, Chemin I. The Hepatitis B Virus Genotypes E to J: The Overlooked Genotypes. Microorganisms 2023; 11:1908. [PMID: 37630468 PMCID: PMC10459053 DOI: 10.3390/microorganisms11081908] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Hepatitis B virus (HBV) genotypes E to J are understudied genotypes. Genotype E is found almost exclusively in West Africa. Genotypes F and H are found in America and are rare in other parts of the world. The distribution of genotype G is not completely known. Genotypes I and J are found in Asia and probably result from recombination events with other genotypes. The number of reported sequences for HBV genotypes E to J is small compared to other genotypes, which could impact phylogenetic and pairwise distance analyses. Genotype F is the most divergent of the HBV genotypes and is subdivided into six subgenotypes F1 to F6. Genotype E may be a recent genotype circulating almost exclusively in sub-Saharan Africa. Genotype J is a putative genotype originating from a single Japanese patient. The paucity of data from sub-Saharan Africa and Latin America is due to the under-representation of these regions in clinical and research cohorts. The purpose of this review is to highlight the need for further research on HBV genotypes E to J, which appear to be overlooked genotypes.
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Affiliation(s)
- Rayana Maryse Toyé
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1052, Centre de Recherche en Cancérologie de Lyon (CRCL), 151 Cours Albert Thomas, 69003 Lyon, France; (R.M.T.); (F.Z.)
| | - Carmen Luisa Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela; (C.L.L.); (R.C.J.)
| | - Rossana Celeste Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela; (C.L.L.); (R.C.J.)
| | - Fabien Zoulim
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1052, Centre de Recherche en Cancérologie de Lyon (CRCL), 151 Cours Albert Thomas, 69003 Lyon, France; (R.M.T.); (F.Z.)
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela; (C.L.L.); (R.C.J.)
- Collégium de Lyon, Institut d’Etudes Avancées, Université Lyon 2, 69007 Lyon, France
| | - Isabelle Chemin
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1052, Centre de Recherche en Cancérologie de Lyon (CRCL), 151 Cours Albert Thomas, 69003 Lyon, France; (R.M.T.); (F.Z.)
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Balde T, Ostankova YV, Boumbaly S, Naidenova EV, Zueva EB, Serikova EN, Valutite DE, Schemelev AN, Davydenko VS, Esaulenko EV, Totolian AA. [Frequency of drug resistance and immune escape mutations in the hepatitis B virus genome detected in pregnant women in the Republic of Guinea]. Vopr Virusol 2023; 68:228-241. [PMID: 37436414 DOI: 10.36233/0507-4088-175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Indexed: 07/13/2023]
Abstract
The aim of the work is to assess the prevalence of hepatitis B virus drug resistance mutations and immune escape mutations in pregnant women in the Republic of Guinea. MATERIALS AND METHODS Blood plasma samples obtained from 480 pregnant women from different regions of the Republic of Guinea with laboratory-confirmed viral hepatitis B were studied. Nucleotide sequences for genotype identification and mutation detection were obtained using nested-PCR followed by Sanger sequencing, based on overlapping pairs of primers spanning the complete genome of the virus. RESULTS AND DISCUSSION In the examined group, the viral genotype E was the most prevalent (92.92%) compared with subgenotypes A1 (1.67%), A3 (1.46%), D1 (0.63%), D2 (1.04%) and D3 (2.29%). Among the examined HBV-infected pregnant women, 188 (39.17%) had undetectable HBsAg. Drug resistance mutations were detected in 33 individuals, which amounted to 6.88%. The following mutations were found: S78T (27.27%), L80I (24.24%), S202I (15.15%), M204I/V (42.42%). The presence of polymorphic variants not described as drug resistant has also been shown in positions associated with the development of drug resistance to tenofovir, lamivudine, telbivudine and entecavir (L80F, S202I, M204R). When analyzing the MHR and the region of a determinant, mutations were detected in 318 (66.25%) of pregnant women. In 172 of them, which amounted to 54.09%, multiple mutations were found. The amino acid substitutions in 13 positions associated with HBsAg-negative hepatitis B and/or potentially affecting HBsAg antigenicity were identified. CONCLUSION The high prevalence of immune escape and drug resistance mutations potentially associated with false-negative result of HBsAg screening, prophylaxis failure, and virological failure of therapy that has been identified among treatment naive pregnant women imposes a serious problem.
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Affiliation(s)
- T Balde
- Research Institute of Applied Biology of Guinea
| | | | - S Boumbaly
- Research Institute of Applied Biology of Guinea
- Centre International de Recherche sur les Infections Tropicales en Guinée
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6
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Ostankova YV, Shchemelev AN, Boumbaly S, Balde TAL, Zueva EB, Valutite DE, Serikova EN, Davydenko VS, Skvoroda VV, Vasileva DA, Semenov AV, Esaulenko EV, Totolian AA. Prevalence of HIV and Viral Hepatitis Markers among Healthcare Workers in the Republic of Guinea. Diagnostics (Basel) 2023; 13:diagnostics13030378. [PMID: 36766482 PMCID: PMC9914033 DOI: 10.3390/diagnostics13030378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
Healthcare workers are much more likely to be infected with HIV and hepatitis viruses compared to the general population. Although healthcare workers are more aware of HIV and hepatitis viruses, several countries in Africa lack a comprehensive grasp of disease routes and transmission risks. The aim of this study was to assess the prevalence of the serological and molecular biological markers of HIV and viral hepatitis among healthcare workers in the Republic of Guinea. The study material was 74 blood serum samples collected from healthcare workers who received additional training at the Institute of Applied Biological Research of Guinea (IRBAG, Kindia, Republic of Guinea). The markers examined included HBsAg, HBeAg, anti-HBs IgG, anti-HBcore IgG, anti-HCV qualitative determination, anti-HEV IgM and IgG, anti-HAV IgM and IgG, and anti-HIV. For viral DNA and RNA detection, nucleic acids were extracted from blood serum, and viral presence was inferred using real-time PCR with hybridization fluorescence detection. A high prevalence of viral hepatitis B markers was shown, and significantly fewer cases of viral hepatitis C and HIV were detected. Almost all examined medical workers had anti-HAV IgG antibodies, but no antibodies to hepatitis E virus. Apparently, the identified markers depend on the general prevalence of certain pathogens in the region and are associated with the traditions and characteristics of the country's residents.
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Affiliation(s)
- Yulia V Ostankova
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Alexander N Shchemelev
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Sanaba Boumbaly
- Institute of Applied Biological Research of Guinea (IRBAG), Kindia 100 BP 75, Guinea
- Centre International de Recherche sur les Infections Tropicales en Guinée, Nzerekore 400 BP, Guinea
| | - Thierno A L Balde
- Institute of Applied Biological Research of Guinea (IRBAG), Kindia 100 BP 75, Guinea
| | - Elena B Zueva
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Diana E Valutite
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Elena N Serikova
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Vladimir S Davydenko
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Vsevolod V Skvoroda
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Daria A Vasileva
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Alexander V Semenov
- Ekaterinburg Research Institute of Viral Infections, State Research Center of Virology and Biotechnology Vector of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 620030 Ekaterinburg, Russia
| | - Elena V Esaulenko
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
| | - Areg A Totolian
- Saint Petersburg Pasteur Institut of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor), 197101 Saint Petersburg, Russia
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Lourenço J, McNaughton AL, Pley C, Obolski U, Gupta S, Matthews PC. Polymorphisms predicting phylogeny in hepatitis B virus. Virus Evol 2022; 9:veac116. [PMID: 36628296 PMCID: PMC9825179 DOI: 10.1093/ve/veac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/30/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B viruses (HBVs) are compact viruses with circular genomes of ∼3.2 kb in length. Four genes (HBx, Core, Surface, and Polymerase) generating seven products are encoded on overlapping reading frames. Ten HBV genotypes have been characterised (A-J), which may account for differences in transmission, outcomes of infection, and treatment response. However, HBV genotyping is rarely undertaken, and sequencing remains inaccessible in many settings. We set out to assess which amino acid (aa) sites in the HBV genome are most informative for determining genotype, using a machine learning approach based on random forest algorithms (RFA). We downloaded 5,496 genome-length HBV sequences from a public database, excluding recombinant sequences, regions with conserved indels, and genotypes I and J. Each gene was separately translated into aa, and the proteins concatenated into a single sequence (length 1,614 aa). Using RFA, we searched for aa sites predictive of genotype and assessed covariation among the sites with a mutual information-based method. We were able to discriminate confidently between genotypes A-H using ten aa sites. Half of these sites (5/10) sites were identified in Polymerase (Pol), of which 4/5 were in the spacer domain and one in reverse transcriptase. A further 4/10 sites were located in Surface protein and a single site in HBx. There were no informative sites in Core. Properties of the aa were generally not conserved between genotypes at informative sites. Among the highest co-varying pairs of sites, there were fifty-five pairs that included one of these 'top ten' sites. Overall, we have shown that RFA analysis is a powerful tool for identifying aa sites that predict the HBV lineage, with an unexpectedly high number of such sites in the spacer domain, which has conventionally been viewed as unimportant for structure or function. Our results improve ease of genotype prediction from limited regions of HBV sequences and may have future applications in understanding HBV evolution.
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Affiliation(s)
| | | | - Caitlin Pley
- Guy’s and St Thomas’ NHS Foundation Trust, Westminster Bridge Rd, London SE1 7EH, UK
| | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv 6997801, Israel,Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
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Maepa MB, Ely A, Kramvis A, Bloom K, Naidoo K, Simani OE, Maponga TG, Arbuthnot P. Hepatitis B Virus Research in South Africa. Viruses 2022; 14:v14091939. [PMID: 36146747 PMCID: PMC9503375 DOI: 10.3390/v14091939] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/11/2022] [Accepted: 08/26/2022] [Indexed: 11/18/2022] Open
Abstract
Despite being vaccine-preventable, hepatitis B virus (HBV) infection remains the seventh leading cause of mortality in the world. In South Africa (SA), over 1.9 million people are chronically infected with HBV, and 70% of all Black chronic carriers are infected with HBV subgenotype A1. The virus remains a significant burden on public health in SA despite the introduction of an infant immunization program implemented in 1995 and the availability of effective treatment for chronic HBV infection. In addition, the high prevalence of HIV infection amplifies HBV replication, predisposes patients to chronicity, and complicates management of the infection. HBV research has made significant progress leading to better understanding of HBV epidemiology and management challenges in the SA context. This has led to recent revision of the national HBV infection management guidelines. Research on developing new vaccines and therapies is underway and progress has been made with designing potentially curative gene therapies against HBV. This review summarizes research carried out in SA on HBV molecular biology, epidemiology, treatment, and vaccination strategies.
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Affiliation(s)
- Mohube B. Maepa
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, Infectious Diseases and Oncology Research Institute (IDORI), University of the Witwatersrand, Johannesburg 2000, South Africa
- Correspondence:
| | - Abdullah Ely
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, Infectious Diseases and Oncology Research Institute (IDORI), University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Anna Kramvis
- Hepatitis Diversity Research Unit, Department of Internal Medicine, Faculty of Health Sciences, School of Clinical Medicine, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, Infectious Diseases and Oncology Research Institute (IDORI), University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Kubendran Naidoo
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, Infectious Diseases and Oncology Research Institute (IDORI), University of the Witwatersrand, Johannesburg 2000, South Africa
- National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Omphile E. Simani
- HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Tongai G. Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7602, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, Infectious Diseases and Oncology Research Institute (IDORI), University of the Witwatersrand, Johannesburg 2000, South Africa
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Application Effect and Accuracy Analysis of Electrochemiluminescence Immunoassay and Enzyme-Linked Immunosorbent Assay in the Serological Test of Hepatitis B Virus. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:9371497. [PMID: 35966724 PMCID: PMC9371851 DOI: 10.1155/2022/9371497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022]
Abstract
Objective To explore the validity and accuracy of electrochemiluminescence immunoassay (ECLIA) and enzyme-linked immunosorbent assay (ELISA) in the serological detection of the hepatitis B virus. Methods From 6 February 2019 to 1 March 2020, 96 patients diagnosed with hepatitis B virus infection in our hospital were recruited and assigned at a ratio of 1 : 1 to experimental groups A (GA) and B (GB), with 48 cases in each group, and the five major serological indicators of hepatitis B were tested and analyzed using ECLIA and ELISA. In addition, 50 suspected patients were selected for two tests, respectively, to compare the accuracy of the two test methods. Results ECLIA was associated with significantly higher expression levels and higher detection rates of HBeAg, HBeAb, HBsAg, and HBsAb versus ELISA (P < 0.05), and the difference in the expression and detection rates of HBcAb levels between the two groups did not come up to the statistical standard (P > 0.05). ECLIA yielded significantly higher sensitivity and specificity than ELISA (P < 0.05), while the two methods showed comparable detection accuracy (P > 0.05). Conclusion Despite the inconsistent results of the latest studies on the serological detection of hepatitis B by the two techniques, ECLIA is consistently superior to ELISA and provides better diagnostic benefits and merits promotion.
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10
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Uche EI, Chukwukaodinaka NE, Akinbami AA, Adeyemi OI, Hassan AO, Bamiro RA, Ibrahim IN, Suleiman AM, Augustine B, Anaduaka DC. Common hepatitis B virus genotypes among blood donors in Lagos, Nigeria. Niger Postgrad Med J 2022; 29:228-235. [PMID: 35900459 DOI: 10.4103/npmj.npmj_19_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is one of the public health diseases causing global health problems. It is a leading cause of cirrhosis and hepatocellular carcinoma. Blood transfusion is a major route of its transmission and screening of blood is suboptimal in our environment. Occult HBV infection describes the presence of HBV DNA in blood or liver tissue in patients who are hepatitis B surface antigen (HBsAg) seronegative. This study documented the common genotypes of HBV a blood-borne infection in the population of blood donors in Lagos. METHODS This was a cross-sectional study carried out at the blood donor clinics of ten Lagos State Government-owned hospitals in Lagos State. A total of 1400 participants were recruited consecutively from November 2020 to June 2021. All participants' samples were screened using Diaspot Rapid Test Kit (RTK) and Dialabenzyme enzyme-linked immunosorbent assay (ELISA) kit. Furthermore, some of the plasma samples were used for HBV DNA extraction and genotyping using the real time-polymerase chain reaction. Statistical analysis was carried out using the Statistical Package for the Social Sciences (SPSS) software version 26 and P value was considered significant at ≤0.05. RESULTS The sero-prevalence of HBsAg using RTK and ELISA was 19.9% and 22.4%, respectively. The prevalence of occult HBV infection was 5.2%. A total of 278 and 313 HBsAg RTK and ELISA positive samples were obtained, respectively. HBV genotype result had A (46.6%) as the most prevalent followed closely by B (44.7%), E (23.8%), D (20.9%) and C (11.2%). CONCLUSION HBV infection has a high prevalence among blood donors. ELISA is a more sensitive screening tool and its use should be advocated nationally. HBV genotype A is the most prevalent genotype from our study.
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Affiliation(s)
- Ebele I Uche
- Department of Haematology and Blood Transfusion, Lagos State University College of Medicine, Lagos, Nigeria
| | - Nwakaego E Chukwukaodinaka
- Department of Haematology and Blood Transfusion, Lagos State University Teaching Hospital, Lagos, Nigeria
| | - Akinsegun A Akinbami
- Department of Haematology and Blood Transfusion, Lagos State University College of Medicine, Lagos, Nigeria
| | - Oluwatosin I Adeyemi
- Department of Haematology and Blood Transfusion, Lagos State University Teaching Hospital, Lagos, Nigeria
| | - Aderonke O Hassan
- Department of Haematology and Blood Transfusion, Lagos State University Teaching Hospital, Lagos, Nigeria
| | - Rafah A Bamiro
- Department of Haematology and Blood Transfusion, Lagos State University Teaching Hospital, Lagos, Nigeria
| | - Ismaila Nda Ibrahim
- Department of Haematology and Blood Transfusion, Ahmadu Bello University, Zaria, Kaduna, Nigeria
| | - Aisha M Suleiman
- Department of Haematology and Blood Transfusion, Ahmadu Bello University, Zaria, Kaduna, Nigeria
| | - Benjamin Augustine
- Department of Haematology and Blood Transfusion, Ahmadu Bello University, Zaria, Kaduna, Nigeria
| | - Doris Chinyelu Anaduaka
- Department of Haematology and Blood Transfusion, Lagos State University Teaching Hospital, Lagos, Nigeria
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11
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Pley C, Lourenço J, McNaughton AL, Matthews PC. Spacer Domain in Hepatitis B Virus Polymerase: Plugging a Hole or Performing a Role? J Virol 2022; 96:e0005122. [PMID: 35412348 PMCID: PMC9093120 DOI: 10.1128/jvi.00051-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Hepatitis B virus (HBV) polymerase is divided into terminal protein, spacer, reverse transcriptase, and RNase domains. Spacer has previously been considered dispensable, merely acting as a tether between other domains or providing plasticity to accommodate deletions and mutations. We explore evidence for the role of spacer sequence, structure, and function in HBV evolution and lineage, consider its associations with escape from drugs, vaccines, and immune responses, and review its potential impacts on disease outcomes.
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Affiliation(s)
- Caitlin Pley
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Anna L. McNaughton
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Nuffield Department of Medicine, University of Oxford Medawar Building, Oxford, United Kingdom
| | - Philippa C. Matthews
- Nuffield Department of Medicine, University of Oxford Medawar Building, Oxford, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
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12
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Ingasia LAO, Wose Kinge C, Kramvis A. Genotype E: The neglected genotype of hepatitis B virus. World J Hepatol 2021; 13:1875-1891. [PMID: 35069995 PMCID: PMC8727212 DOI: 10.4254/wjh.v13.i12.1875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/15/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) (sub)genotypes A1, D3 and E circulate in sub-Saharan Africa, the region with one of the highest incidences of HBV-associated hepatocellular carcinoma globally. Although genotype E was identified more than 20 years ago, and is the most widespread genotype in Africa, it has not been extensively studied. The current knowledge status and gaps in its origin and evolution, natural history of infection, disease progression, response to antiviral therapy and vaccination are discussed. Genotype E is an African genotype, with unique molecular characteristics that is found mainly in Western and Central Africa and rarely outside Africa except in individuals of African descent. The low prevalence of this genotype in the African descendant populations in the New World, phylogeographic analyses, the low genetic diversity and evidence of remnants of genotype E in ancient HBV samples suggests the relatively recent re-introduction into the population. There is scarcity of information on the clinical and virological characteristics of genotype E-infected patients, disease progression and outcomes and efficacy of anti-HBV drugs. Individuals infected with genotype E have been characterised with high hepatitis B e antigen-positivity and high viral load with a lower end of treatment response to interferon-alpha. A minority of genotype E-infected participants have been included in studies in which treatment response was monitored. Of concern is that current guidelines do not consider patients infected with genotype E. Thus, there is an urgent need for further large-scale investigations into genotype E, the neglected genotype of HBV.
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Affiliation(s)
- Luicer Anne Olubayo Ingasia
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, Gauteng, South Africa
| | - Constance Wose Kinge
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, Gauteng, South Africa
- Department of Implementation Science, Right to Care, Johannesburg 0046, Gauteng, South Africa
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, Gauteng, South Africa
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13
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Athamneh RY, Arıkan A, Sayan M, Mahafzah A, Sallam M. Variable Proportions of Phylogenetic Clustering and Low Levels of Antiviral Drug Resistance among the Major HBV Sub-Genotypes in the Middle East and North Africa. Pathogens 2021; 10:1333. [PMID: 34684283 PMCID: PMC8540944 DOI: 10.3390/pathogens10101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022] Open
Abstract
Hepatitis B virus (HBV) infection remains a major public health threat in the Middle East and North Africa (MENA). Phylogenetic analysis of HBV can be helpful to study the putative transmission links and patterns of inter-country spread of the virus. The objectives of the current study were to analyze the HBV genotype/sub-genotype (SGT) distribution, reverse transcriptase (RT), and surface (S) gene mutations and to investigate the domestic transmission of HBV in the MENA. All HBV molecular sequences collected in the MENA were retrieved from GenBank as of 30 April 2021. Determination of genotypes/SGT, RT, and S mutations were based on the Geno2pheno (hbv) 2.0 online tool. For the most prevalent HBV SGTs, maximum likelihood phylogenetic analysis was conducted to identify the putative phylogenetic clusters, with approximate Shimodaira-Hasegawa-like likelihood ratio test values ≥ 0.90, and genetic distance cut-off values ≤ 0.025 substitutions/site as implemented in Cluster Picker. The total number of HBV sequences used for genotype/SGT determination was 4352 that represented a total of 20 MENA countries, with a majority from Iran (n = 2103, 48.3%), Saudi Arabia (n = 503, 11.6%), Tunisia (n = 395, 9.1%), and Turkey (n = 267, 6.1%). Genotype D dominated infections in the MENA (86.6%), followed by genotype A (4.1%), with SGT D1 as the most common in 14 MENA countries and SGT D7 dominance in the Maghreb. The highest prevalence of antiviral drug resistance was observed against lamivudine (4.5%) and telbivudine (4.3%). The proportion of domestic phylogenetic clustering was the highest for SGT D7 (61.9%), followed by SGT D2 (28.2%) and genotype E (25.7%). The largest fraction of domestic clusters with evidence of inter-country spread within the MENA was seen in SGT D7 (81.3%). Small networks (containing 3-14 sequences) dominated among domestic phylogenetic clusters. Specific patterns of HBV genetic diversity were seen in the MENA with SGT D1 dominance in the Levant, Iran, and Turkey; SGT D7 dominance in the Maghreb; and extensive diversity in Saudi Arabia and Egypt. A low prevalence of lamivudine, telbivudine, and entecavir drug resistance was observed in the region, with almost an absence of resistance to tenofovir and adefovir. Variable proportions of phylogenetic clustering indicated prominent domestic transmission of SGT D7 (particularly in the Maghreb) and relatively high levels of virus mobility in SGT D1.
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Affiliation(s)
- Rabaa Y. Athamneh
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (R.Y.A.); (A.A.)
| | - Ayşe Arıkan
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (R.Y.A.); (A.A.)
- DESAM, Near East University, Nicosia 99138, Cyprus;
| | - Murat Sayan
- DESAM, Near East University, Nicosia 99138, Cyprus;
- Clinical Laboratory, PCR Unit, Faculty of Medicine, Kocaeli University, İzmit 41380, Turkey
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Amman 11942, Jordan;
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Amman 11942, Jordan;
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22184 Malmö, Sweden
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Cruz JNMD, Villar LM, Mello FCDA, Lampe E, Hyppolito EB, Lima JMDC, Hyppolito SB, Pires Neto RDJ, Nicolete LDDF, Coelho ICB. Hepatitis B virus genotypes prevalence in patients from hepatology services in Ceará, Brazil. Rev Soc Bras Med Trop 2021; 54:e08072020. [PMID: 34495262 PMCID: PMC8437444 DOI: 10.1590/0037-8682-0807-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 07/16/2021] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Hepatitis B virus (HBV) infection is a public health problem; therefore, we aimed to report HBV genotypes in Ceará, Brazil. METHODS A total of 103 HBsAg-positive samples were subjected to HBV genotyping and subgenotyping. RESULTS The following genetic compositions of samples were found: F-54% (F2-83.33%), A-40% (A1-65%), D-6%, C2-1%, E-1%, and G-1%. CONCLUSIONS Some genotypes are only prevalent in certain parts of the world; however, the State of Ceará is a hub for migration and has one of the most important liver transplantation centers in Brazil, which can explain the prevalence of the F genotype.
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Affiliation(s)
- José Napoleão Monte Da Cruz
- Universidade Federal do Ceará, Departamento de Patologia, Programa de Pós-Graduação em Patologia, Fortaleza, CE, Brasil
| | - Lívia Melo Villar
- Fundação Oswaldo Cruz, Laboratório de Hepatites Virais, Rio de Janeiro, RJ, Brasil
| | | | - Elisabeth Lampe
- Fundação Oswaldo Cruz, Laboratório de Hepatites Virais, Rio de Janeiro, RJ, Brasil
| | | | | | - Silvia Bomfim Hyppolito
- Universidade Federal do Ceará, Maternidade Escola Assis Chateaubriant, Fortaleza, CE, Brasil
| | - Roberto Da Justa Pires Neto
- Hospital São José, Fortaleza, CE, Brasil.,Universidade Federal do Ceará, Departamento de Saúde Comunitária, Fortaleza, CE, Brasil
| | | | - Ivo Castelo Branco Coelho
- Universidade Federal do Ceará, Departamento de Patologia, Programa de Pós-Graduação em Patologia, Fortaleza, CE, Brasil
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15
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Wang R, Xie Z. A Simple and Rapid Method for Quantitative Detection of Hepatitis B Virus Drug-resistant Mutations. J Clin Transl Hepatol 2021; 9:139-140. [PMID: 34007793 PMCID: PMC8111115 DOI: 10.14218/jcth.2021.00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/04/2022] Open
Affiliation(s)
- Ran Wang
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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