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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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Montoya-Guzman M, Martinez J, Castro-Arroyave D, Rojas C, Navas MC. Epidemiology and Genetic Diversity of Hepatitis B Virus and Hepatitis Delta Virus Infection in Indigenous Communities in Colombia. Microorganisms 2023; 11:1739. [PMID: 37512911 PMCID: PMC10386745 DOI: 10.3390/microorganisms11071739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Despite the universal vaccination program, there are still regions and territories with a high prevalence of Hepatitis B Virus infection (HBV), such as the Amazon basin, where several indigenous communities live. Additionally, Hepatitis Delta Virus (HDV) is a defective that requires the hepatitis B surface antigen (HBsAg) for the assembly and release of de novo viral particles. Therefore, hepatitis D could be the result of HBV/HDV coinfection or HDV superinfection in individuals with chronic hepatitis B. Among the high prevalence HDV populations are indigenous communities of America. This study aims to describe and characterize the frequency of HBV and HDV infection, viral genotypes and HBV immune escape mutants in indigenous populations from different regions of Colombia. The diagnosis of hepatitis B and hepatitis D was confirmed by serological markers. Moreover, the HBV and HDV genome were amplified by PCR and RT-PCR, respectively, and, subsequently, the phylogenetic analysis was performed. We characterized 47 cases of chronic hepatitis B, 1 case of reactivation and 2 cases of occult hepatitis B infection (OBI). Furthermore, a high prevalence of HDV infection was identified in the study population (29.33%, 22/75) and the circulation of several HBV genotypes and subgenotypes (F1b, F3, F4, and D). Interestingly, this is the first report of the HDV genotype I circulation in this country. These findings demonstrated that HBV and HDV infections are still public health problems in indigenous communities in Colombia.
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Affiliation(s)
- Melissa Montoya-Guzman
- Grupo Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Jaime Martinez
- Grupo Epidemiología, Facultad Nacional de Salud Pública, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Diana Castro-Arroyave
- Grupo de Estudio en Pedagogía, Infancia y Desarrollo Humano (GEPIDH), Facultad de Educación, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Carlos Rojas
- Grupo Epidemiología, Facultad Nacional de Salud Pública, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
| | - Maria-Cristina Navas
- Grupo Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia
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Sant'Anna TB, Araujo NM. Hepatitis B Virus Genotype D: An Overview of Molecular Epidemiology, Evolutionary History, and Clinical Characteristics. Microorganisms 2023; 11:1101. [PMID: 37317074 PMCID: PMC10221421 DOI: 10.3390/microorganisms11051101] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 06/16/2023] Open
Abstract
The hepatitis B virus (HBV) genotype D (HBV/D) is the most extensively distributed genotype worldwide with distinct molecular and epidemiological features. This report provides an up-to-date review on the history of HBV/D subgenotyping and misclassifications, along with large-scale analysis of over 1000 HBV/D complete genome sequences, with the aim of gaining a thorough understanding of the global prevalence and geographic distribution of HBV/D subgenotypes. We have additionally explored recent paleogenomic findings, which facilitated the detection of HBV/D genomes dating back to the late Iron Age and provided new perspectives on the origins of modern HBV/D strains. Finally, reports on distinct disease outcomes and responses to antiviral therapy among HBV/D subgenotypes are discussed, further highlighting the complexity of this genotype and the importance of HBV subgenotyping in the management and treatment of hepatitis B.
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Affiliation(s)
- Thaís B Sant'Anna
- Laboratory of Molecular Virology and Parasitology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21041-250, RJ, Brazil
| | - Natalia M Araujo
- Laboratory of Molecular Virology and Parasitology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21041-250, RJ, Brazil
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Castro GM, Sosa MJ, Sicilia PE, Riberi MI, Moreno C, Cattaneo R, Debes JD, Barbás MG, Cudolá AE, Pisano MB, Ré VE. Acute and chronic HBV infection in central Argentina: High frequency of sub-genotype F1b, low detection of clinically relevant mutations and first evidence of HDV. Front Med (Lausanne) 2023; 9:1057194. [PMID: 36698842 PMCID: PMC9868314 DOI: 10.3389/fmed.2022.1057194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023] Open
Abstract
Introduction Genomic analysis of hepatitis B virus (HBV) identifies phylogenetic variants, which may lead to distinct biological and clinical behaviors. The satellite hepatitis D virus (HDV) may also influence clinical outcomes in patients with hepatitis B. The aim of this study was to investigate HBV genetic variants, including clinically relevant mutations, and HDV infection in acute and chronic hepatitis B patients in central Argentina. Methods A total of 217 adult HBV infected patients [acute (AHB): n = 79; chronic (CHB): n = 138] were studied; 67 were HBV/human immunodeficiency virus (HIV) coinfected. Clinical and demographic data were obtained from medical records. Serological markers were determined. Molecular detection of HBV and HDV was carried out by RT-Nested PCR, followed by sequencing and phylogenetic analysis. Results Overall, genotype (gt) F [sub-genotype (sgt) F1b] was the most frequently found. In AHB patients, the gts/sgts found were: F1b (74.7%) > A2 (13.9%) > F4 (7.6%) > C (2.5%) > A1 (1.3%). Among CHB patients: F1b (39.1%) > A2 (23.9%) > F4 (18.2%) > D (9.4%) > C and F6 (3.6% each) > A1, A3 and B2 (0.7% each). The distribution of sgt A2 and gt D was significantly different between HBV mono and HBV/HIV coinfected patients [A2: 15.9% vs. 35.7% (p < 0.05), respectively and D: 14.6% vs. 1.8% (p < 0.05), respectively]. Mutation frequency in basal core promoter/pre-Core (BCP/pC) region was 35.5% (77/217) [AHB: 20.3% (16/79), CHB: 44.2% (61/138)]. In the open reading frame (ORF) S, mutations associated with vaccine escape and diagnostic failure were detected in 7.8% of the sequences (17/217) [AHB: 3.8% (3/79), CHB: 10.1% (14/138)]. ORF-P amino acid substitutions associated with antiviral resistance were detected in 3.2% of the samples (7/217) [AHB: 1.3% (1/79), CHB 4.3%, (6/138)]. The anti-HDV seropositivity was 5.2% (4/77); one sample could be sequenced, belonging to gt HDV-1 associated with sgt HBV-D3. Discussion We detected an increase in the circulation of genotype F in Central Argentina, particularly among AHB patients, suggesting transmission advantages over the other genotypes. A low rate of mutations was detected, especially those with antiviral resistance implications, which is an encouraging result. The evidence of HDV circulation in our region, reported for the first time, alerts the health system for its search and diagnosis.
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Affiliation(s)
- Gonzalo M. Castro
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina,*Correspondence: Gonzalo M. Castro,
| | - María J. Sosa
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Paola E. Sicilia
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - María I. Riberi
- Laboratorio de Virología, Servicio de Microbiología, Clínica Universitaria Reina Fabiola, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Claudia Moreno
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Rodolfo Cattaneo
- Servicio de Gastroenterología, Hospital Rawson, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - José D. Debes
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - María G. Barbás
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - Analía E. Cudolá
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina
| | - María B. Pisano
- Laboratorio de Hepatitis Virales, Instituto de Virología “Dr. J. M. Vanella” (InViV)–CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
| | - Viviana E. Ré
- Laboratorio de Hepatitis Virales, Instituto de Virología “Dr. J. M. Vanella” (InViV)–CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
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Marcelino R, Ezeonwumelu IJ, Janeiro A, Mimoso P, Matos S, Briz V, Pimentel V, Pingarilho M, Tato Marinho R, Maria Marcelino J, Taveira N, Abecasis A. Phylogeography of hepatitis B virus: The role of Portugal in the early dissemination of HBV worldwide. PLoS One 2022; 17:e0276618. [PMID: 36548381 PMCID: PMC9778982 DOI: 10.1371/journal.pone.0276618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
In Portugal, the genetic diversity, origin of HBV and the Portuguese role in the dissemination of HBV worldwide were never investigated. In this work, we studied the epidemic history and transmission dynamics of HBV genotypes that are endemic in Portugal. HBV pol gene was sequenced from 130 patients followed in Lisbon. HBV genotype A was the most prevalent (n = 54, 41.5%), followed by D (n = 44, 33.8%), and E (n = 32, 24.6%). Spatio-temporal evolutionary dynamics was reconstructed in BEAST using a Bayesian Markov Chain Monte Carlo method, with a GTR nucleotide substitution model, an uncorrelated lognormal relaxed molecular clock model, a Bayesian skyline plot, and a continuous diffusion model. HBV subgenotype D4 was the first to be introduced in Portugal around 1857 (HPD 95% 1699-1931) followed by D3 and A2 a few decades later. HBV genotype E and subgenotype A1 were introduced in Portugal later, almost simultaneously. Our results indicate a very important role of Portugal in the exportation of subgenotypes D4 and A2 to Brazil and Cape Verde, respectively, in the beginning of the XX century. This work clarifies the epidemiological history of HBV in Portugal and provides new insights in the early and global epidemic history of this virus.
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Affiliation(s)
- Rute Marcelino
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
- Faculdade de Farmácia, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Lisboa, Portugal
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
- * E-mail:
| | - Ifeanyi Jude Ezeonwumelu
- AIDS Research Institute-IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - André Janeiro
- Faculdade de Medicina de Lisboa, GenoMed–Diagnósticos de Medicina Molecular, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Paula Mimoso
- Faculdade de Medicina de Lisboa, GenoMed–Diagnósticos de Medicina Molecular, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Sónia Matos
- Faculdade de Medicina de Lisboa, GenoMed–Diagnósticos de Medicina Molecular, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Veronica Briz
- Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Rui Tato Marinho
- Department of Gastroenterology and Hepatology, Santa Maria Hospital, Medical School of Universidade de Lisboa, Portugal
| | - José Maria Marcelino
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
- Faculdade de Farmácia, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Lisboa, Portugal
| | - Nuno Taveira
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
- Faculdade de Farmácia, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Lisboa, Portugal
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
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Roca TP, Villar LM, Nogueira Lima FS, Vasconcelos MPA, Borzacov LMP, Silva EDCE, do Lago BV, da Silva MTL, Botelho Souza LF, Salcedo JMV, dos Santos ADO, Vieira DS. Genomic Variability of Hepatitis B Virus Circulating in Brazilian Western Amazon. Viruses 2022; 14:v14102100. [PMID: 36298655 PMCID: PMC9611064 DOI: 10.3390/v14102100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
The emergence of clinically relevant mutations in the hepatitis B virus (HBV) genome has been a matter of great debate because of the possibility of escape from the host’s immune system, the potential to cause more severe progression of liver diseases and the emergence of treatment-resistant variants. Here we characterized the circulating variants of HBV in Rondônia State, in the north of Brazil. Serum samples of 62 chronic HBV carriers were subjected to PCR assays and clinical data were collected. Mutations and genotypes were characterized through direct sequencing. The findings show the presence of subgenotypes A1 (54.83%, 34/62), D3 (16.13%, 10/62), F2 (16.13%, 10/62), A2 (4.84%, 3/62), D2 (3.23%, 2/62), D1 (1.61%, 1/62), D4 (1.61%, 1/62) and F4 (1.61%, 1/62). Deletions in the pre-S2 region were found in 13.79% (8/58) of the samples, mutations in the S gene in 59.68% (37/62) and RT mutations in 48.39% (30/62). We found a variable genotypic distribution in different locations and important mutations related to immune escape and drug resistance in Western Amazonia, which contributed to genetic surveillance and provided important information to help control the disease.
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Affiliation(s)
- Tárcio Peixoto Roca
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation of Rondônia—FIOCRUZ/RO, Porto Velho 76812-245, Brazil
- Correspondence: (T.P.R.); (L.M.V.)
| | - Livia Melo Villar
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
- Correspondence: (T.P.R.); (L.M.V.)
| | - Felipe Souza Nogueira Lima
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation of Rondônia—FIOCRUZ/RO, Porto Velho 76812-245, Brazil
| | | | | | | | - Bárbara Vieira do Lago
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Mayara Torquato Lima da Silva
- Laboratory of Biotechnology and Structural Bioengineering, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Juan Miguel Villalobos Salcedo
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation of Rondônia—FIOCRUZ/RO, Porto Velho 76812-245, Brazil
- Tropical Medicine Research Center of Rondônia—CEPEM/RO, Porto Velho 76812-329, Brazil
| | | | - Deusilene Souza Vieira
- Laboratory of Molecular Virology, Oswaldo Cruz Foundation of Rondônia—FIOCRUZ/RO, Porto Velho 76812-245, Brazil
- Tropical Medicine Research Center of Rondônia—CEPEM/RO, Porto Velho 76812-329, Brazil
- Postgraduate Program in Experimental Biology, Federal University of Rondônia—PGBIOEXP/UNIR, Porto Velho 76801-059, Brazil
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7
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Santos Alves FAGD, Nogueira Lima FDS, Ribeiro JR, Roca TP, Santos ADOD, Botelho Souza LF, Villalobos-Salcedo JM, Vieira DS. Genetic diversity of HBV in indigenous populations on the border between Brazil and Bolivia. Braz J Infect Dis 2022; 26:102700. [PMID: 36088957 PMCID: PMC9513627 DOI: 10.1016/j.bjid.2022.102700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/27/2022] [Accepted: 08/14/2022] [Indexed: 02/07/2023] Open
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The unexpected high prevalence of HBV subgenotype D4 in patients with chronic hepatitis B in Galicia, a northwestern Spanish region, reflects strong links with Latin America. J Clin Virol 2022; 153:105195. [PMID: 35661583 DOI: 10.1016/j.jcv.2022.105195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/09/2022] [Accepted: 05/28/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) comprises 9 genotypes and multiple subgenotypes that depict differences in geographic distribution, clinical outcome and response to antiviral therapy. However, the molecular epidemiology of HBV geno/subgenotypes is globally scarce. In Spain, HBV genotype D seems to be more prevalent in the northwestern regions compared to the rest of the country for unclear reasons. METHODS HBV genotyping was performed using geno2pheno on a S gene fragment amplified from plasma collected from all chronic hepatitis B individuals attended at one reference hospital in Santiago de Compostela, the Galicia's capital town. Phylogenetic and phylogeographic analyses using a fragment of 345 bp were performed in all viremic specimens. To avoid misleading allocation as consequence of short fragment analysis, several bioinformatic controls were used. RESULTS A total of 320 individuals with persistent serum HBsAg+ and detectable HBV-DNA were seen between 2000 and 2016 (male 68.4%; median age, 52 years-old; native Spaniards 83.8%). HBV genotype distribution was as follows: A 15.3%; B 1.6%; C 2.5%; D 71.6%; E 3.1%; F 2.2%; G 3.1%; and H 0.6%. HBV genotype D was mostly represented by D4 and D2 subgenotypes (33.4% and 15% of total, respectively). Compared to chronic hepatitis B patients with genotypes B, C, E and G, HBV-D4 carriers tended to be older (54.2% had >50 years-old) and HBeAg-negative (85%). Moreover, 43% were female, 4.7% had cirrhosis, 10.2% hepatitis C and 6.4% HIV coinfection. Phylogenetic analyses could be performed on 82 HBV-D4 specimens; and 79 were confirmed as HBV-D4 using PhyML. Phylogeography using FasTree suggested at least two distinct introductions of HBV-D4 in Galicia, one from the Caribbean and South America, and another from India. CONCLUSIONS HBV subgenotype D4 is the most prevalent HBV variant in chronic hepatitis B patients living in the northwest of Spain, representing 33.4% (107/320) of all chronic hepatitis B infections. This rate of HBV-D4 is among the highest reported worldwide. Epidemiological and phylogenetic analyses suggest a strong association with historical migrant exchanges with Latin America, and especially with the Caribbean basin.
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Xu R, Song D, Wang M, Huang J, Liao Q, Shan Z, Rong X, Fu Y. Molecular Epidemiological Characteristics and Risk Factors for Acquiring HBV Among Li Ethnic in Baisha County, Hainan Island-Subgenotype D3 Was First Discovered in China. Front Microbiol 2022; 13:837746. [PMID: 35197959 PMCID: PMC8859303 DOI: 10.3389/fmicb.2022.837746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/14/2022] [Indexed: 12/02/2022] Open
Abstract
The residents of Baisha, a county of Hainan Island, mainly composed of Li ethnic population and relatively closed living environment with its unique geographical location. Our previous study showed that Li ethnic population of Baisha is an endemic center for hepatitis C virus, with significantly higher rates than in other parts of China. However, the epidemiology of HBV in this region remains unclear. Therefore, we conducted a comprehensive epidemiological survey of HBV in Baisha County, including 1,682 Li ethnic residents. The total seropositive rate for HBsAg was 10.2% and was higher than other parts of China. HBV-positive status was associated with the 20–40-year-old group (OR = 1.27, 95%CI 1.04–1.39, P < 0.01) and alcohol consumption (OR = 2.17, 95%CI 1.58–2.99, P < 0.01). Phylogenetic analysis showed that HBV subgenotype D3 was predominant in Baisha County which was first discovered in China, followed by C5, C1, B2, and undetermined subgenotypes which were significantly different from other geographical distribution of main genotypes in China. The most recent common ancestor (tMRCA) of the HBV genotype C in the Li ethnic of Baisha County was 1846 (95%CI: 1739–1932), and Baisha-C5 was earlier than Baisha-C1 and Baisha-C2. Most Baisha-D3 sequences were concentrated in one bundle and unrelated to those D3 genome sequences elsewhere in the world. According to the phylogenetic tree, D3 was introduced into Baisha County in 1884 (95%CI: 1816–1993) and became a local endemic virus. In conclusion, HBV infection in the Li ethnic group is characterized by a high prevalence rate in 20–40-year-old individuals and a unique genotype distribution which were significantly different from other geographical distribution of main genotypes in China, and subgenotype D3 was first discovered in China.
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Affiliation(s)
- Ru Xu
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
- The Key Medical Laboratory of Guangzhou, Guangzhou, China
| | - Dandan Song
- Department of Clinical Laboratory, The Fifth People’s Hospital of Zhuhai, Zhuhai, China
| | - Min Wang
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
- The Key Medical Laboratory of Guangzhou, Guangzhou, China
| | - Jieting Huang
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
- The Key Medical Laboratory of Guangzhou, Guangzhou, China
| | - Qiao Liao
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
- The Key Medical Laboratory of Guangzhou, Guangzhou, China
| | - Zhengang Shan
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
- The Key Medical Laboratory of Guangzhou, Guangzhou, China
| | - Xia Rong
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
- The Key Medical Laboratory of Guangzhou, Guangzhou, China
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- *Correspondence: Xia Rong,
| | - Yongshui Fu
- Institute of Clinical Blood Transfusion, Guangzhou Blood Center, Guangzhou, China
- The Key Medical Laboratory of Guangzhou, Guangzhou, China
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Zhujiang Hospital of Southern Medical University, Guangzhou, China
- Yongshui Fu,
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10
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Athamneh RY, Arıkan A, Sayan M, Mahafzah A, Sallam M. Variable Proportions of Phylogenetic Clustering and Low Levels of Antiviral Drug Resistance among the Major HBV Sub-Genotypes in the Middle East and North Africa. Pathogens 2021; 10:1333. [PMID: 34684283 PMCID: PMC8540944 DOI: 10.3390/pathogens10101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022] Open
Abstract
Hepatitis B virus (HBV) infection remains a major public health threat in the Middle East and North Africa (MENA). Phylogenetic analysis of HBV can be helpful to study the putative transmission links and patterns of inter-country spread of the virus. The objectives of the current study were to analyze the HBV genotype/sub-genotype (SGT) distribution, reverse transcriptase (RT), and surface (S) gene mutations and to investigate the domestic transmission of HBV in the MENA. All HBV molecular sequences collected in the MENA were retrieved from GenBank as of 30 April 2021. Determination of genotypes/SGT, RT, and S mutations were based on the Geno2pheno (hbv) 2.0 online tool. For the most prevalent HBV SGTs, maximum likelihood phylogenetic analysis was conducted to identify the putative phylogenetic clusters, with approximate Shimodaira-Hasegawa-like likelihood ratio test values ≥ 0.90, and genetic distance cut-off values ≤ 0.025 substitutions/site as implemented in Cluster Picker. The total number of HBV sequences used for genotype/SGT determination was 4352 that represented a total of 20 MENA countries, with a majority from Iran (n = 2103, 48.3%), Saudi Arabia (n = 503, 11.6%), Tunisia (n = 395, 9.1%), and Turkey (n = 267, 6.1%). Genotype D dominated infections in the MENA (86.6%), followed by genotype A (4.1%), with SGT D1 as the most common in 14 MENA countries and SGT D7 dominance in the Maghreb. The highest prevalence of antiviral drug resistance was observed against lamivudine (4.5%) and telbivudine (4.3%). The proportion of domestic phylogenetic clustering was the highest for SGT D7 (61.9%), followed by SGT D2 (28.2%) and genotype E (25.7%). The largest fraction of domestic clusters with evidence of inter-country spread within the MENA was seen in SGT D7 (81.3%). Small networks (containing 3-14 sequences) dominated among domestic phylogenetic clusters. Specific patterns of HBV genetic diversity were seen in the MENA with SGT D1 dominance in the Levant, Iran, and Turkey; SGT D7 dominance in the Maghreb; and extensive diversity in Saudi Arabia and Egypt. A low prevalence of lamivudine, telbivudine, and entecavir drug resistance was observed in the region, with almost an absence of resistance to tenofovir and adefovir. Variable proportions of phylogenetic clustering indicated prominent domestic transmission of SGT D7 (particularly in the Maghreb) and relatively high levels of virus mobility in SGT D1.
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Affiliation(s)
- Rabaa Y. Athamneh
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (R.Y.A.); (A.A.)
| | - Ayşe Arıkan
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (R.Y.A.); (A.A.)
- DESAM, Near East University, Nicosia 99138, Cyprus;
| | - Murat Sayan
- DESAM, Near East University, Nicosia 99138, Cyprus;
- Clinical Laboratory, PCR Unit, Faculty of Medicine, Kocaeli University, İzmit 41380, Turkey
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Amman 11942, Jordan;
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Amman 11942, Jordan;
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22184 Malmö, Sweden
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de Bernardi Schneider A, Osiowy C, Hostager R, Krarup H, Børresen M, Tanaka Y, Morriseau T, Wertheim JO. Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype. Front Microbiol 2021; 11:602296. [PMID: 33519744 PMCID: PMC7843931 DOI: 10.3389/fmicb.2020.602296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
A disproportionate number of Greenland's Inuit population are chronically infected with Hepatitis B virus (HBV; 5-10%). HBV genotypes B and D are most prevalent in the circumpolar Arctic. Here, we report 39 novel HBV/D sequences from individuals residing in southwestern Greenland. We performed phylodynamic analyses with ancient HBV DNA calibrators to investigate the origin and relationship of these taxa to other HBV sequences. We inferred a substitution rate of 1.4 × 10-5 [95% HPD 8.8 × 10-6, 2.0 × 10-5] and a time to the most recent common ancestor of 629 CE [95% HPD 37-1138 CE]. The Greenland taxa form a sister clade to HBV/D2 sequences, specifically New Caledonian and Indigenous Taiwanese sequences. The Greenland sequences share amino acid signatures with subgenotypes D1 and D2 and ~97% sequence identity. Our results suggest the classification of these novel sequences does not fit within the current nomenclature. Thus, we propose these taxa be considered a novel quasi-subgenotype.
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Affiliation(s)
| | - Carla Osiowy
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Reilly Hostager
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - Henrik Krarup
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Department of Medical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Clinical Institute, Aalborg University, Aalborg, Denmark
| | - Malene Børresen
- Department of Epidemiological Research, Statens Serum Institut, Copenhagen, Denmark
| | - Yasuhito Tanaka
- Department of Virology & Liver, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Taylor Morriseau
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, San Diego, CA, United States
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12
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Araujo NM, Teles SA, Spitz N. Comprehensive Analysis of Clinically Significant Hepatitis B Virus Mutations in Relation to Genotype, Subgenotype and Geographic Region. Front Microbiol 2020; 11:616023. [PMID: 33381105 PMCID: PMC7767914 DOI: 10.3389/fmicb.2020.616023] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) is a highly variable DNA virus due to its unique life cycle, which involves an error-prone reverse transcriptase. The high substitution rate drives the evolution of HBV by generating genetic variants upon which selection operates. HBV mutants with clinical implications have been documented worldwide, indicating the potential for spreading and developing their own epidemiology. However, the prevalence of such mutants among the different HBV genotypes and subgenotypes has not been systematically analyzed. In the current study, we performed large-scale analysis of 6,479 full-length HBV genome sequences from genotypes A-H, with the aim of gaining comprehensive insights into the relationships of relevant mutations associated with immune escape, antiviral resistance and hepatocellular carcinoma (HCC) development with HBV (sub)genotypes and geographic regions. Immune escape mutations were detected in 10.7% of the sequences, the most common being I/T126S (1.8%), G145R (1.2%), M133T (1.2%), and Q129R (1.0%). HBV genotype B showed the highest rate of escape mutations (14.7%) while genotype H had no mutations (P < 0.001). HCC-associated mutations were detected in 33.7% of the sequences, with significantly higher frequency of C1653T, T1753V and A1762T/G1764A in genotype G than C (P < 0.001). The overall frequencies of lamivudine-, telbivudine-, adefovir-, and entecavir-resistant mutants were 7.3, 7.2, 0.5, and 0.2%, respectively, while only 0.05% showed reduced susceptibility to tenofovir. In particular, the highest frequency of lamivudine-resistant mutations was observed in genotype G and the lowest frequency in genotype E (32.5 and 0.3%; P < 0.001). The prevalence of HBV mutants was also biased by geographic location, with North America identified as one of the regions with the highest rates of immune escape, antiviral resistance, and HCC-associated mutants. The collective findings were discussed in light of natural selection and the known characteristics of HBV (sub)genotypes. Our data provide relevant information on the prevalence of clinically relevant HBV mutations, which may contribute to further improvement of diagnostic procedures, immunization programs, therapeutic protocols, and disease prognosis.
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Affiliation(s)
- Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Sheila A Teles
- Faculty of Nursing, Federal University of Goias, Goiânia, Brazil
| | - Natália Spitz
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
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13
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Tracing back hepatitis B virus genotype D introduction and dissemination in South Brazil. INFECTION GENETICS AND EVOLUTION 2020; 82:104294. [DOI: 10.1016/j.meegid.2020.104294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/04/2020] [Accepted: 03/22/2020] [Indexed: 12/14/2022]
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14
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Liu H, Shen L, Zhang S, Wang F, Zhang G, Yin Z, Qiu F, Liang X, Wang F, Bi S. Complete genome analysis of hepatitis B virus in Qinghai-Tibet plateau: the geographical distribution, genetic diversity, and co-existence of HBsAg and anti-HBs antibodies. Virol J 2020; 17:75. [PMID: 32532295 PMCID: PMC7291583 DOI: 10.1186/s12985-020-01350-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022] Open
Abstract
Background The genetic variation and origin of Hepatitis B Virus (HBV) in Qinghai-Tibet Plateau were poorly studied. The coexistence of HBsAg and anti-HBs has been described as a puzzle and has never been reported in the indigenous population or in recombinant HBV sequences. This study aimed to report geographical distribution, genetic variability and seroepidemiology of HBV in southwest China. Methods During 2014–2017, 1263 HBsAg positive serum were identified and 183 complete genome sequences were obtained. Serum samples were collected from community-based populations by a multistage random sampling method. Polymerase chain reaction (PCR) was used to amplify the HBV complete genome sequences. Then recombination, genetic variability, and serological analysis were performed. Results (1) Of the 1263 HBsAg positive serum samples, there were significant differences between the distribution of seromarkers in Tibet and Qinghai. (2) Of 183 complete genome sequences, there were 130 HBV/CD1 (71.0%), 49 HBV/CD2 (26.8%) and four HBV/C2 isolates (2.2%). Serotype ayw2 (96.1%) was the main serological subtype. (3) Several nucleotide mutations were dramatically different in CD1 and CD2 sequences. Clinical prognosis-related genetic variations such as nucleotide mutation T1762/A1764 (27.93%), A2189C (12.85%), G1613A (8.94%), T1753C (8.38%), T53C (4.47%) T3098C (1.68%) and PreS deletion (2.23%) were detected in CD recombinants. (4) From the inner land of China to the northeast boundary of India, different geographical distributions between CD1 and CD2 were identified. (5) Twenty-seven (2.14%) HBsAg/HBsAb coexistence serum samples were identified. S protein amino acid mutation and PreS deletion were with significant differences between HBsAg/HBsAb coexistence group and control group. Conclusions HBV/CD may have a mixed China and South Asia origin. Based on genetic variations, the clinical prognosis of CD recombinant seems more temperate than genotype C strains in China. The HBsAg/HBsAb coexistence is a result of both PreS deletion and aa variation in S protein. Several unique mutations were frequently detected in HBV/CD isolates, which could potentially influence the clinical prognosis.
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Affiliation(s)
- He Liu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Rd 155#, Changping District, Beijing, China.,Department of Infectious Disease, Tianjin Center for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Liping Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Rd 155#, Changping District, Beijing, China
| | - Shuang Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Rd 155#, Changping District, Beijing, China
| | - Feng Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Rd 155#, Changping District, Beijing, China
| | - Guomin Zhang
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zundong Yin
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Feng Qiu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Rd 155#, Changping District, Beijing, China
| | - Xiaofeng Liang
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Fuzhen Wang
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shengli Bi
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Rd 155#, Changping District, Beijing, China.
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