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Downs LO, McNaughton AL, de Cesare M, Ansari MA, Martin J, Woodrow C, Bowden R, Collier J, Barnes E, Matthews PC. Case Report: Application of hepatitis B virus (HBV) deep sequencing to distinguish between acute and chronic infection. Wellcome Open Res 2021; 5:240. [PMID: 33458253 PMCID: PMC7802106 DOI: 10.12688/wellcomeopenres.16157.2] [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] [Accepted: 01/15/2021] [Indexed: 11/20/2022] Open
Abstract
Deep sequencing of the full-length hepatitis B virus (HBV) genome provides the opportunity to determine the extent to which viral diversity, genotype, polymorphisms, insertions and deletions may influence presentation and outcomes of disease. Increasing experience with analysis of HBV genomic data opens up the potential for using these data to inform insights into pathophysiology of infection and to underpin decision making in clinical practice. We here set out to undertake whole genome HBV sequencing from an adult who presented acutely unwell with a new diagnosis of HBV infection, and tested positive for both HBV anti-core IgM and IgG, possibly representing either acute hepatitis B infection (AHB) or chronic hepatitis B with an acute reactivation (CHB-AR). The distinction between these two scenarios may be important in predicting prognosis and underpinning treatment decisions, but can be challenging based on routine laboratory tests. Through application of deep whole-genome sequencing we typed the isolate as genotype-D1, and identified several minority variants including G1764A and G1986A substitutions in the pre-core promoter and pre-core regions, which support CHB-AR rather than AHB. In the longer term, enhanced deep sequencing data for HBV may provide improved evidence to distinguish between acute and chronic infection, to predict outcomes and to stratify treatment.
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Affiliation(s)
- Louise O. Downs
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Rd, Oxford, OX1 3SY, UK
| | - Anna L. McNaughton
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Rd, Oxford, OX1 3SY, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Wellcome Centre for Human Genetics, Oxford, OX3 9DU, UK
| | - M. Azim Ansari
- Wellcome Centre for Human Genetics, Wellcome Centre for Human Genetics, Oxford, OX3 9DU, UK
| | - Jacqueline Martin
- Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Charles Woodrow
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, Wellcome Centre for Human Genetics, Oxford, OX3 9DU, UK
| | - Jane Collier
- Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Rd, Oxford, OX1 3SY, UK
- Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford NIHR BRC, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Philippa C. Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Rd, Oxford, OX1 3SY, UK
- Oxford NIHR BRC, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
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Downs LO, McNaughton AL, de Cesare M, Ansari MA, Martin J, Woodrow C, Bowden R, Collier J, Barnes E, Matthews PC. Case Report: Application of hepatitis B virus (HBV) deep sequencing to distinguish between acute and chronic infection. Wellcome Open Res 2020; 5:240. [PMID: 33458253 PMCID: PMC7802106 DOI: 10.12688/wellcomeopenres.16157.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2020] [Indexed: 01/01/2024] Open
Abstract
Deep sequencing of the full-length hepatitis B virus (HBV) genome provides the opportunity to determine the extent to which viral diversity, genotype, polymorphisms, insertions and deletions may influence presentation and outcomes of disease. Increasing experience with analysis of HBV genomic data opens up the potential for using these data to inform insights into pathophysiology of infection and to underpin decision making in clinical practice. We here set out to undertake whole genome HBV sequencing from an adult who presented acutely unwell with a new diagnosis of HBV infection, and tested positive for both HBV anti-core IgM and IgG, possibly representing either acute hepatitis B infection (AHB) or chronic hepatitis B with an acute reactivation (CHB-AR). The distinction between these two scenarios may be important in predicting prognosis and underpinning treatment decisions, but can be challenging based on routine laboratory tests. Through application of deep whole-genome sequencing we typed the isolate as genotype-D1, and identified several minority variants including G1764A and G1986A substitutions in the pre-core promoter and pre-core regions, which support CHB-AR rather than AHB. In the longer term, enhanced deep sequencing data for HBV may provide improved evidence to distinguish between acute and chronic infection, to predict outcomes and to stratify treatment.
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Affiliation(s)
- Louise O. Downs
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Rd, Oxford, OX1 3SY, UK
| | - Anna L. McNaughton
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Rd, Oxford, OX1 3SY, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Wellcome Centre for Human Genetics, Oxford, OX3 9DU, UK
| | - M. Azim Ansari
- Wellcome Centre for Human Genetics, Wellcome Centre for Human Genetics, Oxford, OX3 9DU, UK
| | - Jacqueline Martin
- Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Charles Woodrow
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, Wellcome Centre for Human Genetics, Oxford, OX3 9DU, UK
| | - Jane Collier
- Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Rd, Oxford, OX1 3SY, UK
- Department of Hepatology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford NIHR BRC, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Philippa C. Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Rd, Oxford, OX1 3SY, UK
- Oxford NIHR BRC, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
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Ko K, Takahashi K, Nagashima S, Yamamoto C, Ork V, Sugiyama A, Akita T, Ohisa M, Chuon C, Hossain MS, Mao B, Tanaka J. Existence of hepatitis B virus surface protein mutations and other variants: demand for hepatitis B infection control in Cambodia. BMC Infect Dis 2020; 20:305. [PMID: 32334529 PMCID: PMC7183719 DOI: 10.1186/s12879-020-05025-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/12/2020] [Indexed: 12/16/2022] Open
Abstract
Background This study aimed to detect Hepatitis B virus (HBV) genome sequences and their variants as of nationwide scale using dried blood spot (DBS) samples and to provide up-to-date reference data for infection control and surveillance in Cambodia. Method Among 2518 children age 5–7 years and their 2023 mothers participated in 2017 Cambodia nationwide sero-survey on hepatitis B surface antigen (HBsAg) prevalence using multistage random sampling strategy, 95 mothers and 13 children positive to HBsAg were included in this study. HBV DNA was extracted from DBS, then performed polymerase chain reaction. HBV genotypes and potential variants were examined by partial and full length genomic analysis. Results HBsAg positive rate was 4.7% (95/2023) in mothers and 0.52% (13/2518) in their children. Genotype C (80.49%) was abundantly found throughout the whole Cambodia whilst genotype B (19.51%) was exclusively found in regions bordering Vietnam. S gene mutants of HBV were found in 24.29% of mothers and 16.67% of children with HBV DNA positive sera. Full-length genome analysis revealed the homology of 99.62–100% in each mother-child pair. Genotype B was clarified to recombinant genotype B4/C2 and B2/C2. Double (48.39%) and combination mutation (32.26%) were observed in core promoter region of HBV C1 strains. Conclusions This study showed the capable of DBS for large-scale molecular epidemiological study of HBV in resource limited countries. Full-genome sequences yield the better understanding of sub-genotypes, their variants and the degree of homology between strains isolated from mother-child pairs calls for effective strategies on prevention, control and surveillance of mother-to-child HBV transmission in Cambodia.
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Affiliation(s)
- Ko Ko
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kazuaki Takahashi
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Shintaro Nagashima
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Chikako Yamamoto
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Vichit Ork
- National Immunization Programme, Ministry of Health, 151-152 Kampuchea Krom Avenue, Phonm Penh, Cambodia
| | - Aya Sugiyama
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Tomoyuki Akita
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Masayuki Ohisa
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Channarena Chuon
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Md Shafiqul Hossain
- Expanded Programme on Immunization, World Health Organization Country Office, Cambodia; 61-64, Preah Norodom Blvd (St 306), Sangkat Boeung Keng Kang I, Khan Chamkamom, Phnom Penh, Cambodia
| | - Bunsoth Mao
- University of Health Sciences, 73 Monivong Boulevard, Phnom Penh, Cambodia
| | - Junko Tanaka
- Department of Epidemiology, Infectious Disease Control and Prevention, Hiroshima University Graduate School of Biomedical and Health Sciences, Japan; 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
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Characteristics and evolutionary history of hepatitis B virus quasi-subgenotype B3 in Southeast Asia. Virus Res 2019; 273:197762. [PMID: 31541667 DOI: 10.1016/j.virusres.2019.197762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 12/16/2022]
Abstract
To analyze the hepatitis B virus (HBV) quasi-subgenotype B3 characters and molecular evolution in Southeast Asia, 411 serum samples with HBsAg positive were collected from Xishuangbanna, China. After DNA extraction, PCR amplification and sequencing, a total of 183 HBV full-length genomes were obtained. Phylogenetic analysis showed 139 stains (76.0%) were genotype B, 41 strains were genotype C (22.4%) and 3 strains were genotype I (1.6%). Among genotype B, 34 sequences were identified as quasi-subgenotype B3. Quasi-subgenotype B3 sequences from this study and quasi-subgenotype B3 sequences from the GenBank (total of 141 complete genome sequences) were grouped into quasi-subgenotype B3 (B3, formerly B5, Chinese B6 and B7-9). Sixteen peculiar nucleotides distributed in quasi-subgenotype B3 were identified, which were differ from B1, B2, B4 and B5(formerly B6) (nt93 T, nt100C, nt355 G, nt843 T, nt861C, nt912C, nt929 T, nt930 G, nt1023 T, nt1041 T, nt2651C, nt2693 T, nt2970C, nt3054A, nt3087A and nt3171 G). Then Evolutionary dynamics analysis of HBV quasi-subgenotype B3 was performed. The mean rate of nucleotide substitution for HBV quasi-subgenotype B3 was estimated to be around 5.556-5.660 × 10-4 substitutions/site/year. Estimated time to most recent ancestor of quasi-subgenotype B3 was around the 1847-1945(95%HPD), and Yunnan strains might be the parental strains. The Bayesian sky plot showed a steady spreading of HBV quasi-genotype B3 from early of 1940s to 90 s. In summary, HBV quasi-subgenotype B3 infection is prevalent in Southeast Asia based on the current reports and still with a high prevalence rate based on the evolutionary dynamics analysis. Current vaccine and nucleotide analogues might have effective prevention and treatment for HBV quasi-subgenotype B3 based on the rare clinically relevant mutation sites included in quasi-subgenotype B3.
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Luo D, Liu Y, Chen R, Niu M, Liu L, Li X, Li Q, Huang B, Wang J, Xu D, Lin S. Investigation of hepatitis B virus (HBV) rtS78T/sC69* mutation in a large cohort of chronic HBV-infected patients with nucleoside/nucleotide analogue treatment. Antiviral Res 2019; 170:104579. [PMID: 31398372 DOI: 10.1016/j.antiviral.2019.104579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/29/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023]
Abstract
This study aimed to investigate clinical occurrence and significance of the rtS78T/sC69* mutation of hepatitis B virus (HBV). A total of 22,009 consecutive chronic HBV-infected patients who underwent resistance testing at the Fifth Medical Center of Chinese PLA General Hospital (Original name Beijing 302 Hospital) from 2007 to 2016 were enrolled. Serum samples were collected for sequence analysis of HBV reverse-transcriptase (RT) and S regions. Phenotypic analysis was performed to evaluate the viral replication capacity and drug susceptibility. The rtS78T mutation was detected in 0.83% (182/22,009) of the patients' samples. All mutations simultaneously created a stop codon at sC69 (sC69*). The prevalence of rtS78T/sC69* did not differ significantly between the patients with and without entecavir/tenofovir treatment. Of the 182 mutation-positive samples, 41 (22.5%) were detected with signature drug-resistance mutations to adefovir (n = 26), lamivudine (n = 11), entecavir (n = 3), and lamivudine plus adefovir (n = 1). The HBV DNA and RNA levels of the rtS78T/sC69* mutant were significantly increased compared to the wild-type; while the mutant had undetectable secreted and intracellular HBsAg, and its half maximal effective concentration to lamivudine, adefovir, entecavir, and tenofovir were 3.73-, 1.61-, 4.76-, and 3.71-fold of the wild-type, respectively. Artificial elimination of the rtS78T mutation had a limited effect on the drug susceptibilities. The data obtained in the present study suggested that the emergence of the rtS78T/sC69* mutation was not closely related to entecavir/tenofovir treatment and itself appeared insufficient to confer drug resistance unless it coexisted with signature drug-resistance mutations.
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Affiliation(s)
- Dan Luo
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China; Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Yan Liu
- Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Rongjuan Chen
- Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Ming Niu
- Institute of Chinese Medicine, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Lujie Liu
- Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Xiaodong Li
- Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Qi Li
- Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Bixia Huang
- Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Jun Wang
- Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China
| | - Dongping Xu
- Institute of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital (Beijing 302 Hospital), Beijing, 100039, China.
| | - Shumei Lin
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
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Mijočević H, Karimzadeh H, Seebach J, Usman Z, Al-Mahtab M, Bazinet M, Vaillant A, Roggendorf M. Variants of hepatitis B virus surface antigen observed during therapy with nucleic acid polymer REP 2139-Ca have no influence on treatment outcome and its detection by diagnostic assays. J Viral Hepat 2019; 26:485-495. [PMID: 30450662 DOI: 10.1111/jvh.13044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022]
Abstract
The treatment of patients suffering from HBeAg-positive chronic hepatitis B with REP 2139-Ca resulted in potent reductions in HBsAg and HBV DNA, seroconversion to anti-HBs and the establishment of functional control of infection. In this cohort of 12 patients, we investigated whether differences between HBsAg sequences might explain the lack of response to REP 2139-Ca observed in 3 of 12 patients. We also assessed if the reduction or complete loss of HBsAg in serum observed during therapy were caused by mutations in the "a" determinant preventing the detection of HBsAg by standard diagnostic assays. The complete pre-S/S open reading frame (ORF) was sequenced and pre-S1, pre-S2 and S amino acid sequences were analysed. We found no major differences between pre-S1, pre-S2 and S sequences in responders and nonresponders correlated with low reduction in HBsAg. In addition, we found no mutations in the "a" determinant that would significantly affect the reactivity of HBsAg in diagnostic assays. These results demonstrate that the amino acid sequence of complete pre-S/S ORF has no direct influence on response to REP 2139-Ca therapy.
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Affiliation(s)
- Hrvoje Mijočević
- Institute of Virology, Technische Universität München, Munich, Germany
| | - Hadi Karimzadeh
- Institute of Virology, Technische Universität München, Munich, Germany.,Department of Medicine II, University Hospital Munich-Grosshadern, Munich, Germany
| | - Judith Seebach
- Institute of Virology, Technische Universität München, Munich, Germany
| | - Zainab Usman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Mamun Al-Mahtab
- Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
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Choga WT, Anderson M, Zumbika E, Moyo S, Mbangiwa T, Phinius BB, Melamu P, Kayembe MK, Kasvosve I, Sebunya TK, Blackard JT, Essex M, Musonda RM, Gaseitsiwe S. Molecular characterization of hepatitis B virus in blood donors in Botswana. Virus Genes 2018; 55:33-42. [PMID: 30382563 DOI: 10.1007/s11262-018-1610-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/25/2018] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) poses a significant threat to blood transfusion safety in sub-Saharan Africa (SSA) where allogeneic blood donations are screened serologically, and more sensitive nucleic acid tests (NATs) are utilized infrequently. HBV strains circulating among blood donors in Botswana are not yet characterized. We designed a cross-sectional study to determine the HBV sub-genotypes and prevalence of hepatitis B surface antigen (HBsAg) among blood donors between November 2014 and October 2015. A total of 12,575 blood donations were screened for HBsAg and 50 consecutive plasma samples were selected for genotyping from confirmed HBsAg+ donations. Overlapping Pol and complete S (Pol/S) open reading frames (ORFs) were sequenced from extracted HBV DNA. To identify any signature amino acids, mutations were compared to sequences from a cohort of chronic HBV patients co-infected with HIV and were treatment naïve. The prevalence of HBsAg+ blood donors was 1.02% (95% CI 0.9-1.2%), and the circulating sub-genotypes were A1 serotype adw2 (36.1%), D2 serotype ayw2 (2.9%), and D3 serotypes ayw 1/2 (58.3%). Prevalence of escape mutations was 14% from HBV isolates of blood donors and 15% from isolates of HBV/HIV co-infected patients (p = 0.6926). The escape mutations sP120L, sG130R, sY134H, and sD144A were identified predominantly among HBV isolates from blood donors. These escape mutations have been associated with accelerated HBV sequelae [e.g., liver cirrhosis (LC) and hepatocellular carcinoma (HCC)], failure to detect HBsAg, inability to respond to immunoglobulin (Ig) therapy, and HBV vaccine escape. Characterizing the HBV burden, circulating sub-genotypes, and clinically relevant mutations among blood donors in Botswana is important to elucidate the efficacy of currently available vaccines, predicting HBV-transmission patterns, understanding the cohort's risk to HBV-related complications, and to developing prevention strategies and effective genotype-based antiretroviral therapies.
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Affiliation(s)
- Wonderful T Choga
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Motswedi Anderson
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Edward Zumbika
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Sikhulile Moyo
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tshepiso Mbangiwa
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Bonolo B Phinius
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Pinkie Melamu
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Mukendi K Kayembe
- National Health Laboratory (NHL), Ministry of Health and Wellness, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Theresa K Sebunya
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Jason T Blackard
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Max Essex
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rosemary M Musonda
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Private Bag BO 320, Gaborone, Botswana.
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8
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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: 4.1] [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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Abstract
BACKGROUND The long-term use of nucleos(t)ide analogues causes drug resistance and mutations in the HBV reverse transcriptase (RT) region of the polymerase gene. The RT region overlaps the HBV surface gene (S gene) and therefore, the mutations in the RT region simultaneously modify S gene sequence. Certain mutations in the RT region bring about truncated S proteins because the corresponding changed S gene encodes a stop codon which results in the loss of a large portion of the C-terminal hydrophobic region of HBV surface protein. The rtA181T/sW172*, rtM204I/sW196* and rtV191I/sW182* are the most frequently reported drug-resistant mutations with C-terminal truncation, these mutations have oncogenic potential. DATA SOURCES PubMed and Web of Science were searched using terms: "hepatitis B virus", "HBV drug resistance mutation", "HBV surface protein", "HBV truncation", "hepatocellular carcinoma", "rtA181T/sW172*", "rtM204I/sW196*", "rtV191I/sW182*", and relevant articles published in English in the past decades were reviewed. RESULTS The rtA181T/sW172* and rtV191I/sW182* mutants occurred more frequently than the rtM204I/sW196* mutant both in chronic hepatitis B patients and the HBV-related hepatocellular carcinoma tissues. Although these mutations occur naturally, nucleos(t)ide analogues therapy is the main driving force. These mutations may exist alone or coexist with other HBV mutations. All these three mutants impair the virion secretion and result in HBV surface protein retention and serum HBV DNA level reduction. These mutations possess potential carcinogenic properties. The three mutations are resistant to more than one nucleos(t)ide analogue and therefore, it is difficult to treat the patients with the truncated mutations. CONCLUSIONS Nucleos(t)ide analogues induce drug resistance and HBV S gene truncated mutations. These mutations have potential carcinogenesis.
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Affiliation(s)
- Meng-Lan Wang
- Center of Infectious Diseases, West China Hospital of Sichuan University; Division of Infectious Diseases, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
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Araujo NM. Hepatitis B virus intergenotypic recombinants worldwide: An overview. INFECTION GENETICS AND EVOLUTION 2015; 36:500-510. [PMID: 26299884 DOI: 10.1016/j.meegid.2015.08.024] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/11/2015] [Accepted: 08/19/2015] [Indexed: 02/07/2023]
Abstract
Novel variants generated by recombination events between different hepatitis B virus (HBV) genotypes have been increasingly documented worldwide, and the role of recombination in the evolutionary history of HBV is of significant research interest. In the present study, large-scale data retrieval and analysis on HBV intergenotypic recombinant genomes were performed. The geographical distribution of HBV recombinants as well as the molecular processes involved in recombination were examined. After review of published data, a total of 436 complete HBV sequences, previously identified as recombinants, were included in the recombination detection analysis. About 60% of HBV recombinants were B/C (n=179) and C/D (n=83) hybrids. A/B/C, A/C, A/C/G, A/D, A/E, A/G, B/C/U (U=unknown genotype), C/F, C/G, C/J, D/E, D/F, and F/G hybrids were additionally identified. HBV intergenotypic sequences were reported in almost all geographical regions with similar circulation patterns as their original genotypes, indicating the potential for spreading in a wide range of human populations and developing their own epidemiology. Recombination breakpoints were non-randomly distributed in the genome, and specific favored sites detected, such as within nt 1700-2000 and 2100-2300 regions, which displayed a statistically significant difference in comparison with the remaining genome. Elucidation of the effects of recombination events on the evolutionary history of HBV is critical to understand current and future evolution trends.
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Affiliation(s)
- Natalia M Araujo
- Laboratório de Virologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, 21040-360 Rio de Janeiro, RJ, Brazil.
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Croagh CM, Desmond PV, Bell SJ. Genotypes and viral variants in chronic hepatitis B: A review of epidemiology and clinical relevance. World J Hepatol 2015; 7:289-303. [PMID: 25848459 PMCID: PMC4381158 DOI: 10.4254/wjh.v7.i3.289] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/04/2014] [Accepted: 12/29/2014] [Indexed: 02/06/2023] Open
Abstract
The Hepatitis B Virus (HBV) has a worldwide distribution and is endemic in many populations. It is constantly evolving and 10 genotypic strains have been identified with varying prevalences in different geographic regions. Numerous stable mutations in the core gene and in the surface gene of the HBV have also been identified in untreated HBV populations. The genotypes and viral variants have been associated with certain clinical features of HBV related liver disease and Hepatocellular carcinoma. For example Genotype C is associated with later hepatitis B e antigen (HBeAg) seroconversion, and more advanced liver disease. Genotype A is associated with a greater risk of progression to chronicity in adult acquired HBV infections. Genotype D is particularly associated with the precore mutation and HBeAg negative chronic hepatitis B (CHB). The genotypes prevalent in parts of West Africa, Central and South America, E, F and H respectively, are less well studied. Viral variants especially the Basal Core Promotor mutation is associated with increased risk of fibrosis and cancer of the liver. Although not currently part of routine clinical care, evaluation of genotype and viral variants may provide useful adjunctive information in predicting risk about liver related morbidity in patients with CHB.
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Affiliation(s)
- Catherine Mn Croagh
- Catherine MN Croagh, Paul V Desmond, Sally J Bell, Department of Gastroenterology, St Vincent's Hospital, Fitzroy, Victoria 3065, Australia
| | - Paul V Desmond
- Catherine MN Croagh, Paul V Desmond, Sally J Bell, Department of Gastroenterology, St Vincent's Hospital, Fitzroy, Victoria 3065, Australia
| | - Sally J Bell
- Catherine MN Croagh, Paul V Desmond, Sally J Bell, Department of Gastroenterology, St Vincent's Hospital, Fitzroy, Victoria 3065, Australia
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Naturally occurring hepatitis B virus surface antigen mutant variants in Malaysian blood donors and vaccinees. Eur J Clin Microbiol Infect Dis 2015; 34:1349-59. [PMID: 25792010 PMCID: PMC4475248 DOI: 10.1007/s10096-015-2358-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/25/2015] [Indexed: 12/18/2022]
Abstract
Hepatitis B virus surface mutants are of enormous importance because they are capable of escaping detection by serology and can infect both vaccinated and unvaccinated populations, thus putting the whole population at risk. This study aimed to detect and characterise hepatitis B-escaped mutants among blood donors and vaccinees. One thousand serum samples were collected for this study from blood donors and vaccinees. Hepatitis B surface antigen, antibodies and core antibodies were tested using a commercial enzyme-linked immunosorbent assay (ELISA) kit. DNA detection was performed via nested polymerase chain reaction (PCR), and the S gene was sequenced and analysed using bioinformatics. Of the 1,000 samples that were screened, 5.5 % (55/1,000) were found to be HBsAg-negative and anti-HBc- and HBV DNA-positive. All 55 isolates were found to belong to genotype B. Several mutations were found across all the sequences from synonymous and non-synonymous mutations, with the most nucleotide mutations occurring at position 342, where adenine was replaced by guanine, and cytosine at position 46 was replaced by adenine in 96.4 % and 98 % of the isolates, respectively. Mutation at position 16 of the amino acid sequence was found to be common to all the Malaysian isolates, with 85.7 % of the mutations occurring outside the major hydrophilic region. This study revealed a prevalence of 5.5 % for hepatitis B-escaped mutations among blood donors and vaccinated undergraduates, with the most common mutation being found at position 16, where glutamine was substituted with lysine.
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13
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Epidemiology of HBV subgenotypes D. Clin Res Hepatol Gastroenterol 2015; 39:28-37. [PMID: 25037178 DOI: 10.1016/j.clinre.2014.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/09/2014] [Accepted: 06/02/2014] [Indexed: 02/04/2023]
Abstract
The natural history of hepatitis B virus infection is not uniform and affected from several factors including, HBV genotype. Genotype D is a widely distributed genotype. Among genotype D, several subgenotypes differentiate epidemiologically and probably clinically. D1 is predominant in Middle East and North Africa, and characterized by early HBeAg seroconversion and low viral load. D2 is seen in Albania, Turkey, Brazil, western India, Lebanon, and Serbia. D3 was reported from Serbia, western India, and Indonesia. It is a predominant subgenotype in injection drug use-related acute HBV infections in Europe and Canada. D4 is relatively rare and reported from Haiti, Russia and Baltic region, Brazil, Kenya, Morocco and Rwanda. Subgenotype D5 seems to be common in Eastern India. D6 has been reported as a rare subgenotype from Indonesia, Kenya, Russia and Baltic region. D7 is the main genotype in Morocco and Tunisia. D8 and D9 are recently described subgenotypes and reported from Niger and India, respectively. Subgenotypes of genotype D may have clinical and/or viral differences. More subgenotype studies are required to conclude on subgenotype and its clinical/viral characteristics.
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Suppiah J, Mohd Zain R, Haji Nawi S, Bahari N, Saat Z. Drug-resistance associated mutations in polymerase (p) gene of hepatitis B virus isolated from malaysian HBV carriers. HEPATITIS MONTHLY 2014; 14:e13173. [PMID: 24497877 PMCID: PMC3909636 DOI: 10.5812/hepatmon.13173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/09/2013] [Accepted: 11/01/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Mutations in the polymerase (P) gene of hepatitis B virus are often associated with drug resistance. The pattern of mutations varies geographically, thus giving rise to genotypes diversity. OBJECTIVES This study was carried out to detect mutations in P gene of hepatitis B virus isolated from Malaysian HBV carriers. MATERIALS AND METHODS A total of 58 sera samples were analyzed by PCR and sequencing, of which the P gene of isolated HBV was successfully amplified and sequenced from 40 samples. RESULTS Genotyping of these samples revealed that the predominant genotype was genotype C (22/40, 55.0%), followed by genotype B (17/40, 42.5%), and only 1 sample showed genotype D (2.5%). A number of significant drug resistant mutations were found in five patients including S202I, N236T, M250L, L180M/V, M204I, A181T, T184G, M250V, and V173L. Of these, L180M/V and M204I were most frequently detected (80%) and associated with lamivudine in combination with emtricitabine and telbivudine drug resistance. Association with age, sex, and clinical symptoms revealed that these patients were all male, mid to elderly age and almost all hadcirrhotic liver disease. CONCLUSIONS Detection and surveillance of the significant sites of mutations in HBV is crucial for clinicians to decide on the choice of antiviral treatment and further management of hepatitis B carriers.
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Affiliation(s)
- Jeyanthi Suppiah
- Virology Unit, Institute for Medical Research, Kuala Lumpur, Malaysia
- Corresponding Author: Jeyanthi Suppiah, Virology Unit, Institute for Medical Research, Jln Pahang, 50588, Kuala Lumpur, Malaysia. Tel/Fax: +60-326162674, E-mail:
| | | | | | | | - Zainah Saat
- Virology Unit, Institute for Medical Research, Kuala Lumpur, Malaysia
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Amino acid similarities and divergences in the small surface proteins of genotype C hepatitis B viruses between nucleos(t)ide analogue-naïve and lamivudine-treated patients with chronic hepatitis B. Antiviral Res 2013; 102:29-34. [PMID: 24316031 DOI: 10.1016/j.antiviral.2013.11.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/06/2013] [Accepted: 11/28/2013] [Indexed: 02/06/2023]
Abstract
Entire C-genotype small hepatitis B surface (SHBs) sequences were isolated from 139 nucleos(t)ide analogues (NA)-naïve and 74 lamivudine (LMV)-treated chronic hepatitis B (CHB) patients. The conservation and variability of total 226 amino acids (AAs) within the sequences were determined individually, revealing significant higher mutant isolate rate and mutation frequency in LMV-treated cohort than those in the NA-naïve one (P=0.009 and 0.0001, respectively). Three absolutely conserved fragments (s16-s19, s176-s181 and s185-s188) and seven moderately conserved regions (a few AA sites acquiring increased variability after LMV-treatment) were identified. The significant mutation rate increase after LMV-treatment occurred primarily in major hydrophilic region (except 'a' determinant) and transmembrane domain 3/4, but not in other upstream functional regions of SHBs. With little influence on immune escape-associated mutation frequencies within 'a' determinant, LMV-monotherapy significantly induced classical LMVr-associated mirror changes sE164D/rtV173L, sI195M/rtM204V and sW196L/S/rtM204I, as well as non-classical ones sG44E/rtS53N, sT47K/A/rtH55R/Q and sW182stop/rtV191I outside 'a' determinant. Interestingly, another newly-identified truncation mutation sC69stop/rtS78T decreased from 7.91% (11/139) in NA-naïve cohort to 2.70% (2/74) in LMV-treated one. Altogether, the altered AA conservation and diversity in SHBs sequences after LMV-treatment in genotype-C HBV infection might shed new insights into how LMV-therapy affects the SHBs variant evolution and its antigenicity.
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Forbi JC, Ben-Ayed Y, Xia GL, Vaughan G, Drobeniuc J, Switzer WM, Khudyakov YE. Disparate distribution of hepatitis B virus genotypes in four sub-Saharan African countries. J Clin Virol 2013; 58:59-66. [PMID: 23871163 DOI: 10.1016/j.jcv.2013.06.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/23/2013] [Accepted: 06/21/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) places a substantial health burden on Africa. Here, we investigated genetic diversity of HBV variants circulating in 4 countries of sub-Saharan Africa using archived samples. In total, 1492 plasma samples were tested from HIV-infected individuals and pregnant women, among which 143 (9.6%) were PCR-positive for HBV DNA (Côte d'Ivoire, 70/608 [11.5%]; Ghana, 13/444 [2.9%]; Cameroon, 33/303 [10.9%]; and Uganda, 27/137 [19.7%]). STUDY DESIGN/RESULTS Phylogenetic analysis of the S-gene sequences identified HBV genotypes E (HBV/E, n=96) and A (HBV/A, n=47) distributed as follows: 87% of HBV/E and 13% of HBV/A in Côte d'Ivoire; 100% of HBV/E in Ghana; 67% of HBV/E and 33% of HBV/A in Cameroon; and 100% of HBV/A in Uganda. The average and maximal nucleotide distances among HBV/E sequences were 1.9% and 6.4%, respectively, suggesting a greater genetic diversity for this genotype than previously reported (p<0.001). HBV/A strains were classified into subgenotypes HBV/A1, HBV/A2 and HBV/A3. In Uganda, 93% of HBV/A strains belonged to HBV/A1 whereas HBV/A3 was the only subgenotype of HBV/A found in Cameroon. In Côte d'Ivoire, HBV/A strains were classified as HBV/A1 (11.1%), HBV/A2 (33.3%) and HBV/A3 (55.6%). Phylogeographic analysis of the sequences available from Africa supported earlier suggestions on the origin of HBV/A1, HBV/A2 and HBV/A3 in East, South and West/Central Africa, respectively. Using predicted amino acid sequences, hepatitis B surface antigen (HBsAg) was classified into serotype ayw4 in 93% of HBV/E strains and adw2 in 68% of HBV/A strains. Also, 7.7% of the sequences carried substitutions in HBsAg associated with immune escape. CONCLUSIONS The observations of pan-African and global dissemination of HBV/A1 and HBV/A2, and the circulation of HBV/E and HBV/A3 almost exclusively in West and Central Africa suggest a more recent increase in prevalence in Africa of HBV/E and HBV/A3 compared to HBV/A1 and HBV/A2. The broad genetic heterogeneity of HBsAg detected here may impact the efficacy of prevention and control efforts in sub-Saharan Africa.
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Affiliation(s)
- Joseph C Forbi
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30333, USA.
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Siburian MD, Utama A, Dhenni R, Arnelis N, Fanany I, Intan MDB, Kurniasih TS, Andriani F, Afadlal S, Julianto EB, Rasman WS, Zubir N, Mathew G. High prevalence of hepatitis B virus genotype C/C1 in the Minangkabau ethnic group in Indonesia. Virol J 2013; 10:27. [PMID: 23336976 PMCID: PMC3583810 DOI: 10.1186/1743-422x-10-27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 01/15/2013] [Indexed: 12/13/2022] Open
Abstract
Background The Minangkabau is one of the major ethnic groups in Indonesia. Previous studies with a limited number of samples have shown a different prevalence of HBV/C in the Minangkabau compared to the Indonesian population in general. The aim of this study was to assess the HBV genotype distribution pattern and the prevalence of pre-S, T1753V and A1762T/G1764A mutations among the Minangkabau HBV carriers. The samples were collected from Padang, West Sumatera and from western Java. Mixed primers for specific genotypes were used to determine the HBV genotype. Pre-S or S genes were amplified, sequenced and aligned with reference sequences from GenBank to derive a phylogenetic tree for subgenotyping. Pre-S genes were also analyzed for mutations. The basal core promoter (BCP) region was amplified and directly sequenced to analyze T1753V and A1762T/G1764A mutations. Results The predominant HBV genotype among the Minangkabau HBV carriers (n=117) was C (72.6%) followed by B (24.8%) and co-infection with B and C (2.6%). The prevalence of pre-S mutations, including both the pre-S deletion and pre-S2 start codon mutation, was 41.0%, and the T1753V and A1762T/G1764A mutations were found in 51.9% and 71.2% respectively. HBV/C1 was the predominant HBV subgenotype in the Minangkabau HBV carriers, and was found in 66.2%, followed by B3, B7, C8, B2, B9, C2, and C10 (18.3%, 7.0%, 2.8%, 1.4%, 1.4%, 1.4%, and 1.4% respectively). From samples that were found to be co-infected with HBV B and C, two samples were successfully cloned and subgenotyped, including one with mixed subgenotypes of B3 and C1, and another one with mixed subgenotypes of B7, C1, putative intergenotypic of B/A, and C/A. Furthermore, three samples from donors of non-Minangkabau ethnicity from Padang were found to be infected with an intragenotypic recombination form, including a putative recombinant of B8/B3 and B9/B7. Conclusion HBV/C with subgenotype C1 was the predominant HBV genotype among HBV carriers of Minangkabau ethnicity. The prevalence of pre-S, A1762T/G1764A, and T1753V mutations was higher among the Minangkabau compared to Indonesian HBV carriers in general.
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Affiliation(s)
- Marlinang D Siburian
- Molecular Epidemiology Division, Mochtar Riady Institute for Nanotechnology, Universitas Pelita Harapan, Lippo Karawaci, Tangerang, Indonesia
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Shi W, Carr MJ, Dunford L, Zhu C, Hall WW, Higgins DG. Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis. Virology 2012; 427:51-9. [PMID: 22374235 DOI: 10.1016/j.virol.2012.01.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/14/2012] [Accepted: 01/26/2012] [Indexed: 02/08/2023]
Abstract
Recombination plays an important role in the evolutionary history of Hepatitis B virus (HBV). We performed a phylogenetic analysis of 3403 full-length HBV genome sequences isolated from humans to define the genotype. The genome sequences were divided into 13 sub-datasets, each approximately 250 bp in length. Genotype designations obtained from the sub-datasets that differed from the genotype defined by the whole genome were assigned as putative recombinants. Our results showed that 3379 out of 3403 sequences belonged to the previously described and putative genotypes A to J respectively, with 315 sequences defined in this analysis. The remaining 24 viruses had sequence divergence of less than 8% with both genotypes B and C and were provisionally assigned genotype "BC". 1047 out of 3403 sequences were identified to be putative recombinants, of which 72 were identified to be novel recombinants. Notably, all viruses of the herein described genotype "BC" were identified to be B/C recombinants.
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Affiliation(s)
- Weifeng Shi
- The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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Abstract
BACKGROUND AND AIM To determine the etiology of liver cirrhosis and risk factors for hepatocellular carcinoma (HCC) in a multiracial Asian population. METHODS Consecutive patients with liver cirrhosis presenting to outpatient clinics and inpatient service at the University of Malaya Medical Centre from 1 April 2006 to 31 May 2009 were included. RESULTS A total of 460 patients were included in the study: 317 male patients (68.9%) and 143 female patients (31.1%), with a mean age of 58.8years (range: 15-87years). The major causes of cirrhosis were: chronic hepatitis B, n=212, 46.1%; chronic hepatitis C, n=85, 18.5%; cryptogenic, n=71, 15.4%; alcohol, n=58, 12.6% and autoimmune, n=9, 2.0%. Alcohol was the main etiology in Indians (51.1%) compared to Malay (0%) and Chinese (4.4%) (both P<0.001). Hepatitis B was the predominant etiology in Malay (47.9%) and Chinese (58.8%) compared to Indians (5.6%) (both P<0.001). Hepatitis C cirrhosis was highest in Malays (25.0%). 136 patients (29.6%) had concurrent HCC. Male sex (P<0.001), age>60years (P=0.014), hepatitis B (P<0.001), hepatitis C (P=0.006) and cryptogenic cause (P=0.002) were found to be independent risk factors for HCC. CONCLUSIONS The etiology of cirrhosis has a peculiar pattern based on racial differences in alcohol intake and in the prevalence of hepatitis B.
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Affiliation(s)
- Choon-Seng Qua
- Division of Gastroenterology and Hepatology, University of Malaya, Kuala Lumpur, Malaysia
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Hepatitis B virus (HBV) infection and recombination between HBV genotypes D and E in asymptomatic blood donors from Khartoum, Sudan. J Clin Microbiol 2010; 49:298-306. [PMID: 21048009 DOI: 10.1128/jcm.00867-10] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sudan is a highly endemic area for hepatitis B virus (HBV), and >5% of blood donors are chronically infected. To examine potential strategies to improve HBV blood safety, 404 replacement donor samples previously screened for HBV surface antigen (HBsAg) were tested for antibody to HBV core (anti-HBc), anti-surface antigen (anti-HBs), and HBV DNA. Of 145 anti-HBc-containing samples (36%) identified, 16 retested were HBsAg positive (11%). Anti-HBs was detected in 43/77 (56%) anti-HBc-reactive samples. Six samples were HBsAg(-)/anti-HBc(+)/anti-HBs(+) and contained HBV DNA, meeting the definition of occult HBV infection (OBI). OBIs had low HBV DNA loads (<10 IU/ml) and were genotype B (n = 1) or genotype D (n = 5). Pre-S/S and/or whole genome sequences were obtained from 47 randomly selected HBsAg-positive donors added to the previous 16. Genotype E was identified in 27 strains (57.5%), genotype D in 19 strains (40.5%), and genotype A2 in 1 strain (2%). Two outlier strains within genotype D ultimately were identified as recombinants of genotypes D and E with identical recombination points, suggesting circulating, infectious, recombinant strains. Anti-HBc screening does not appear to be a sustainable blood safety strategy because of the cost and the negative impact on the Sudanese blood supply, even when reduced by anti-HBs testing. Being at the junction between two main African HBV genotypes, genetic recombination occurred and became part of the molecular epidemiology of HBV in Sudan.
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