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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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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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3
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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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4
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Hundie GB, Stalin Raj V, Gebre Michael D, Pas SD, Koopmans MP, Osterhaus ADME, Smits SL, Haagmans BL. A novel hepatitis B virus subgenotype D10 circulating in Ethiopia. J Viral Hepat 2017; 24:163-173. [PMID: 27808472 DOI: 10.1111/jvh.12631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/06/2016] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) is genetically highly divergent and classified in ten genotypes and forty subgenotypes in distinct ethno-geographic populations worldwide. Ethiopia is a country with high HBV prevalence; however, little is known about the genetic variability of HBV strains that circulate. Here, we characterize the complete genome of 29 HBV strains originating from five Ethiopian regions, by 454 deep sequencing and Sanger sequencing. Phylogenetically, ten strains were classified as genotype A1 and nineteen as genotype D. Fifteen genotype D strains, provisionally named subgenotype D10, showed a novel distinct cluster supported by high bootstrap value and >4% nucleotide divergence from other known subgenotypes. In addition, the novel D10 strains harboured nine unique amino acid signatures in the surface, polymerase and X genes. Seventy-two per cent of the genotype D strains had the precore premature stop codon G1896A. In addition, 63% genotype A and 33% genotype D strains had the basal core promoter mutations, A1762T/G1764A. Furthermore, four pre-S deletion variants and two recombinants were identified in this study. In conclusion, we identified a novel HBV subgenotype D10 circulating in Ethiopia, underlining the high genetic variability of HBV strains in Africa.
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Affiliation(s)
- G B Hundie
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - D Gebre Michael
- National blood bank services, Ministry of Health, Addis Ababa, Ethiopia
| | - S D Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M P Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - A D M E Osterhaus
- Artemis One health, Utrecht, The Netherlands.,Center for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
| | - S L Smits
- ViroClinics BioScience BV, Rotterdam, The Netherlands
| | - B L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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5
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Baudi I, Iijima S, Chin'ombe N, Mtapuri-Zinyowera S, Murakami S, Isogawa M, Hachiya A, Iwatani Y, Tanaka Y. Molecular epidemiology of co-infection with hepatitis B virus and human immunodeficiency virus (HIV) among adult patients in Harare, Zimbabwe. J Med Virol 2016; 89:257-266. [PMID: 27458715 DOI: 10.1002/jmv.24641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2016] [Indexed: 12/20/2022]
Abstract
The objective of this study was to determine the prevalence of co-infection with hepatitis B virus (HBV) and human immunodeficiency virus (HIV) and the genetic characteristics of both viruses among pre-HIV-treatment patients in Harare, Zimbabwe. This cross-sectional survey involved 176 remnant plasma samples collected from consenting HIV patients (median age 35 [18-74]) between June and September 2014. HBV seromarkers were determined by high-sensitivity chemiluminescence assays. Molecular evolutionary analyses were conducted on the basal core promoter/precore (BCP/PC) and S regions of HBV, as well as part of the HIV pol region. Of the 176 participants (65.7% female), 19 (10.8%) were positive for HBsAg (median 0.033 IU/ml (IQR 0.01-415). The HBsAg incidence was higher in men than women (P = 0.009). HBsAg-positive subjects had lower median CD4 counts (P = 0.016). HBV DNA was detectable in 12 HBsAg-positive samples (median 3.36 log cp/ml (2.86-4.51), seven being amplified and sequenced. All isolates were subgenotype A1 without HBV drug resistance mutations but each had at least one BCP/PC mutation. PreS deletion mutants and small S antigen variants M133I/T and D144G were identified. Of the 164 HIV isolates successfully genotyped, 163 (99.4%) were HIV-1 subtype C and only one was HIV-1 subtype F1. Sixteen (9.8%) had at least one drug resistance mutation, predominantly non-nucleoside reverse transcriptase inhibitor-related mutations, observed mostly among female participants. This study shows that co-infection with HBV is present among HIV patients enrolling into HIV care in Zimbabwe, suggesting that HBV screening and monitoring programmes be strengthened in this context. J. Med. Virol. 89:257-266, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ian Baudi
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Sayuki Iijima
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Nyasha Chin'ombe
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | | | - Shuko Murakami
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Masanori Isogawa
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Atsuko Hachiya
- National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yasumasa Iwatani
- National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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6
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Hundie GB, Raj VS, Michael DG, Pas SD, Osterhaus ADME, Koopmans MP, Smits SL, Haagmans BL. Molecular epidemiology and genetic diversity of hepatitis B virus in Ethiopia. J Med Virol 2015; 88:1035-43. [PMID: 26629781 DOI: 10.1002/jmv.24437] [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] [Accepted: 11/30/2015] [Indexed: 12/18/2022]
Abstract
Although hepatitis B virus (HBV) infection is hyperendemic in Ethiopia and constitutes a major public health problem, little is known about its genetic diversity, genotypes, and circulation. The aim of this study was to determine the molecular epidemiology and genetic diversity of HBV in Ethiopia, using 391 serum samples collected from HBsAg-positive blood donors living in five different geographic regions. The HBV S/pol gene was amplified, sequenced, and HBV genotypes, subgenotypes, serotypes, and major hydrophilic region (MHR) variants were determined. Phylogenetic analysis of 371 samples (95%) revealed the distribution of genotypes A (78%) and D (22%) in Ethiopia. Further phylogenetic analysis identified one subgenotype (A1) within genotype A, and 4 subgenotypes within genotype D (D1; 1.3%, D2; 55%, D4; 2.5%, and D6; 8.8%). Importantly, 24 isolates (30%) of genotype D formed a novel phylogenetic cluster, distinct from any known D subgenotypes, and two A/D recombinants. Analysis of predicted amino-acid sequences within the HBsAg revealed four serotypes: adw2 (79%), ayw1 (3.1%), ayw2 (7.8%), and ayw3 (11.6%). Subsequent examination of sequences showed that 51 HBV isolates (14%) had mutations in the MHR and 8 isolates (2.2%) in the reverse transcriptase known to confer antiviral resistance. This study provides the first description of HBV genetic diversity in Ethiopia with a predominance of subgenotypes A1 and D2, and also identified HBV isolates that could represent a novel subgenotype. Furthermore, a significant prevalence of HBsAg variants in Ethiopian population is revealed.
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Affiliation(s)
| | - V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.,Division of Virology, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Saskia L Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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Analysis of hepatitis B virus genotypes by restriction fragment length polymorphism. BIOMEDICA 2015; 36:79-88. [DOI: 10.7705/biomedica.v36i0.2976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 12/15/2022]
Abstract
<p><strong>Introducción.</strong> Se han descrito diez genotipos (A-J) del virus de la hepatitis B (HBV) que están distribuidos en todos los continentes. Una de las técnicas utilizadas para determinar el genotipo viral es el análisis del polimorfismo de longitud de los fragmentos de restricción, un método simple y económico, pero con algunas limitaciones.<br /><strong>Objetivo.</strong> El objetivo inicial del estudio fue identificar el genotipo del HBV mediante RFLP en muestras de suero obtenidas de pacientes y donantes de sangre. Sin embargo, por las discrepancias observadas en los patrones de RFLP fue necesario realizar análisis filogenéticos y un análisis in silico de secuencias del HBV.<br /><strong>Materiales y métodos.</strong> Se obtuvieron 56 muestras de suero. Tras la extracción de ADN, se amplificó un fragmento del ORF S del HBV mediante reacción en cadena de la polimerasa, cuyos productos se analizaron por RFLP con las enzimas <em>AlwI</em>, <em>BsrI</em>, <em>CfrI</em>, <em>HpaII</em> y <em>StyI</em>, y algunos se secuenciaron. Los patrones obtenidos se compararon con los reportados previamente. Se efectuó un análisis<em> in silico</em> de RFLP en consideración de las diferencias entre los patrones esperados y los observados.<br /><strong>Resultados.</strong> Se identificaron los genotipos A y F, subgenotipo F3, en las muestras. Este resultado coincide con lo descrito en estudios previos en los que se ha demostrado que el genotipo F, subgenotipo F3, es prevalente en la población de la región andina del país, en tanto que el genotipo A predomina en el occidente (departamento del Chocó). Con base en el análisis <em>in silico</em> de 229 secuencias virales obtenidas del GenBank y las 11 secuencias de este estudio, se caracterizó un nuevo patrón de RFLP específico para el genotipo F, subgenotipo F3, y se describieron algunas modificaciones en el patrón de RFLP del genotipo A, subgenotipo A1.<br /><strong>Conclusiones.</strong> Se caracterizó el patrón de genotipificación del genotipo F, subgenotipo F3, del HBV mediante RFLP, análisis in silico y secuenciación. Se requieren nuevos análisis in silico con un número mayor de secuencias para validar los patrones de RFLP de los genotipos y subgenotipos del VHB.</p>
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Hepatitis B virus infection in post-vaccination South Africa: occult HBV infection and circulating surface gene variants. J Clin Virol 2014; 63:12-7. [PMID: 25600597 DOI: 10.1016/j.jcv.2014.11.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/19/2014] [Accepted: 11/24/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND OBJECTIVE The aim of this study was to investigate the prevalence of occult hepatitis B virus (HBV) infection and the HBV surface (S) gene variants circulating in the South African population after nearly two decades of universal hepatitis B vaccination. STUDY DESIGN From a previous serosurvey, 201 serum samples with serological evidence of exposure to HBV were identified and these were stratified into post- and pre-vaccine introduction populations. For all samples, HBV DNA was screened and quantified using a real-time PCR assay and results analysed together with HBV serological markers. Where HIV results were available, subset analysis was performed. The HBV S gene was PCR-amplified and sequences analysed for a total of 37 isolates. RESULTS The prevalence of occult HBV infection reduced from 70.4% in the pre-vaccine introduction era to 66.0% post-vaccine introduction. There was an association between HIV infection and an increase in prevalence of occult HBV infection within the post-vaccine introduction population, although this was not statistically significant. Furthermore, sequence analysis revealed the following HBV subgenotypes; A1 (n=34), A2 (n=2) and a rare D4 isolate. HBV S gene variants, including diagnostic escape mutants were isolated. CONCLUSION There was a decline in the prevalence of occult HBV infection in post-vaccination South Africa, although the disease burden remains significant in the HIV co-infected population. After nearly two decades of a universal hepatitis B vaccination programme, no positive selection of vaccine escape mutants were observed.
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Yousif M, Mudawi H, Hussein W, Mukhtar M, Nemeri O, Glebe D, Kramvis A. Genotyping and virological characteristics of hepatitis B virus in HIV-infected individuals in Sudan. Int J Infect Dis 2014; 29:125-32. [PMID: 25449246 DOI: 10.1016/j.ijid.2014.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 06/19/2014] [Accepted: 07/02/2014] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) share common routes of blood-borne transmission. In HBV mono-infected Sudanese individuals, genotypes D, E, and A circulate. The objective of this study was to molecularly characterize HBV from HBV/HIV co-infected individuals. METHODS The polymerase overlapping the S region and the basic core promoter (BCP/PC) of HBV from 32 hepatitis B surface antigen (HBsAg)-positive and 18 HBsAg-negative serum samples were amplified and sequenced. RESULTS HBV from 37 samples was successfully genotyped and the genotype distribution was 46.0% D, 21.6% E, 18.9% A, and 13.5% D/E recombinant. Compared to mono-infected individuals, the frequencies of the D/E recombinant and genotype A were higher in HBV/HIV co-infected patients, as was the intra-group divergence of genotype E. BCP/PC mutations affecting hepatitis B e antigen (HBeAg) expression at the transcriptional and translational levels were detected. Two HBsAg-positive individuals had pre-S deletion mutants. The following mutations in the S region could account for the HBsAg negativity: sM133T, sE164G, sV168G, and sS174N. No primary drug resistance mutations were found. CONCLUSIONS In HBV/HIV co-infected Sudanese patients, the ratio of genotype A to non-A was higher than that in mono-infected patients. The genotype E intra-group divergence in HBV/HIV co-infected individuals was significantly higher than that in HBV mono-infected patients.
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Affiliation(s)
- Mukhlid Yousif
- Hepatitis Virus Diversity Research Programme, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
| | - Hatim Mudawi
- Department of Medicine, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Waleed Hussein
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Maowia Mukhtar
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Omer Nemeri
- College of Medicine, Bahri University, Khartoum, Sudan
| | - Dieter Glebe
- Institute of Medical Virology, National Reference Centre of Hepatitis B and D, Justus Liebig-University of Giessen, Giessen, Germany
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Programme, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa.
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Hepatitis B virus subgenotype A1, occurrence of subgenotype D4, and S gene mutations among voluntary blood donors in Kenya. Virus Genes 2013; 47:448-55. [DOI: 10.1007/s11262-013-0976-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/26/2013] [Indexed: 12/18/2022]
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Ochwoto M, Chauhan R, Gopalakrishnan D, Chen CY, Ng'ang'a Z, Okoth F, Kioko H, Kimotho J, Kaiguri P, Kramvis A. Genotyping and molecular characterization of hepatitis B virus in liver disease patients in Kenya. INFECTION GENETICS AND EVOLUTION 2013; 20:103-10. [PMID: 23978387 DOI: 10.1016/j.meegid.2013.08.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/15/2013] [Accepted: 08/18/2013] [Indexed: 12/17/2022]
Abstract
Hepatitis B virus (HBV) genotypes are important in both the clinical manifestation of disease and treatment response. Although Kenya belongs to the African Region (AFR-E) characterized by high mortality and hyperendemicity of HBV, there is a paucity of HBV genotyping data. The aim of this study was to molecularly characterize the basic core promoter/precore (BCP/PC) and complete surface (S) regions of HBV isolated from 61 HBsAg-positive liver disease patients attending Kenyatta National Hospital in Nairobi. HBsAg, HBeAg and viral loads were determined. HBV DNA was amplified and sequenced from 58/61 patients. In addition to the complete genome of two isolates, the BCP/PC and the complete S regions of 43 and 38 isolates, respectively were sequenced. Following phylogenetic analysis of the S region, 38 isolates clustered with subgenotype A1, whereas two isolates clustered with genotype D, one with subgenotype D1 and another as an outlier of the clade containing subgenotype D6 and the D/E recombinant. When the complete genome of the latter isolate was sequenced it clustered with D6. The majority of isolates belonged to serological subtype adw2 and only four to ayw2. Three distinct groups of subgenotype A1, distinguished by different amino acid motifs, circulate in Kenya: two in the African cluster and a monophyletic clade in the "Asian" cluster. HBeAg-negativity was a result of G1896A in genotype D isolates, whereas in subgenotype A1, the HBeAg-negativity was a result of mutations in the Kozak region (1809-1812) or precore start codon (1814-1816). Mutations at positions 1762 and 1764 occurred more frequently in HCC patients (p<0.05). In conclusion, subgenotypes A1, D1 and D6 circulate in liver disease patients in Kenya, with A1 predominating.
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Affiliation(s)
- Missiani Ochwoto
- Hepatitis Virus Diversity Research Programme (HVDRP), Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Kenya Medical Research Institute (KEMRI), Kenya; Jomo Kenyatta University of Agriculture and Technology (JKUAT), Kenya.
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Molecular characterization of hepatitis B virus in liver disease patients and asymptomatic carriers of the virus in Sudan. BMC Infect Dis 2013; 13:328. [PMID: 23865777 PMCID: PMC3722059 DOI: 10.1186/1471-2334-13-328] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 07/16/2013] [Indexed: 12/12/2022] Open
Abstract
Background Hepatitis B virus is hyperendemic in Sudan. Our aim was to molecularly characterize hepatitis B virus from Sudanese individuals, with and without liver disease, because genotypes play an important role in clinical manifestation and treatment management. Methods Ninety-nine patients - 30 asymptomatic, 42 cirrhotic, 15 with hepatocellular carcinoma, 7 with acute hepatitis and 5 with chronic hepatitis- were enrolled. Sequencing of surface and basic core promoter/precore regions and complete genome were performed. Results The mean ± standard deviation, age was 45.7±14.8 years and the male to female ratio 77:22. The median (interquartile range) of hepatitis B virus DNA and alanine aminotransferase levels were 2.8 (2.2-4.2) log IU/ml and 30 (19–49) IU/L, respectively. Using three genotyping methods, 81/99 (82%) could be genotyped. Forty eight percent of the 99 patients were infected with genotype D and 24% with genotype E, 2% with putative D/E recombinants and 7% with genotype A. Patients infected with genotype E had higher frequency of hepatitis B e antigen-positivity and higher viral loads compared to patients infected with genotype D. Basic core promoter/precore region mutations, including the G1896A in 37% of HBeAg-negative individuals, could account for hepatitis B e antigen-negativity. Pre-S deletion mutants were found in genotypes D and E. Three isolates had the vaccine escape mutant sM133T. Conclusion Sudanese hepatitis B virus carriers were mainly infected with genotypes D or E, with patients infected with genotype E having higher HBeAg-positivity and higher viral loads. This is the first study to molecularly characterize hepatitis B virus from liver disease patients in Sudan.
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Kramvis A, Paraskevis D. Subgenotype A1 of HBV--tracing human migrations in and out of Africa. Antivir Ther 2013; 18:513-21. [PMID: 23792935 DOI: 10.3851/imp2657] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND HBV subgenotype A1 is the dominant genotype A strain in Africa, with molecular characteristics differentiating it from A2, which prevails elsewhere. Outside Africa, A1 is confined to areas with migration history from Africa, including India and Latin America. The aim of this study was to reconstruct A1 phylogeny on a spatial scale in order to determine whether A1 can be used to track human migrations. METHODS A phylogenetic comparison of A1 was established using neighbour-joining analysis of complete genomes, and the Bayesian method, implemented in BEAST, was performed on the S region of isolates from 22 countries. Migration events were estimated by ancestral state reconstruction using the criterion of parsimony. RESULTS From the tree reconstruction, nucleotide divergence calculations and migration analysis, it was evident that Africa was the source of dispersal of A1 globally, and its dispersal to Asia and Latin America occurred at a similar time period. Strains from South Africa were the most divergent, clustering in both the African and Asian/American clades and a South African subclade was the origin of A1. The effect of the 9th to 19th century trade and slave routes on the dispersal of A1 was evident and certain unexpected findings, such as the co-clustering of Somalian and Latin American strains, and the dispersal of A1 from India to Haiti, correlated with historical evidence. CONCLUSIONS Phylogeographic analyses of subgenotype A1 can be used to trace human migrations in and out of Africa and the plausible sites of origin and migration routes are presented.
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Affiliation(s)
- Anna Kramvis
- Hepatitis Virus Diversity Research Programme, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Skelton M, Kew MC, Kramvis A. Distinct mutant hepatitis B virus genomes, with alterations in all four open reading frames, in a single South African hepatocellular carcinoma patient. Virus Res 2011; 163:59-65. [PMID: 21889961 DOI: 10.1016/j.virusres.2011.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 08/18/2011] [Accepted: 08/18/2011] [Indexed: 12/27/2022]
Abstract
Sequence variation of hepatitis B virus (HBV) can influence the replication, antigen expression and pathogenicity of the virus. We report on the mutational analysis of HBV performed in a 28-year-old Black South African female diagnosed with HBV-induced hepatocellular carcinoma. Full-genome amplification and DNA sequencing of HBV was carried out. Five distinct complete genomic clones were described with extensive genomic and intragenic variation. Phylogenetic analysis revealed that all five clones belonged to subgenotype A1 and that there were at least four virus populations with genomes of different lengths ranging from 3194 to 3253 base pairs. In this particular patient, four major characteristic features, not previously reported to occur simultaneously in HBV isolated from a single patient, were observed. Firstly, all the clones harboured a 13 base pair deletion and a 45 base pair insertion in the basic core promoter (BCP). Secondly, a 37 base pair insertion in the core gene with three adjacent single nucleotide deletions were observed. Thirdly, premature S gene stop codons were observed in some clones and lastly X gene initiation codon mutations were also observed. The complex nature of the mutations in the HBV isolated from this single patient may have contributed to the early onset of hepatocarcinogenesis.
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Affiliation(s)
- Michelle Skelton
- Hepatitis Virus Diversity Research Programme (formerly MRC/CANSA/University Molecular Hepatology Research Unit), Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg 2193, South Africa.
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