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Dopico E, Vila M, Tabernero D, Gregori J, Rando-Segura A, Pacín-Ruíz B, Guerrero L, Ubillos I, Martínez MJ, Costa J, Quer J, Pérez-Garreta J, González-Sánchez A, Antón A, Pumarola T, Riveiro-Barciela M, Ferrer-Costa R, Buti M, Rodríguez-Frías F, Cortese MF. Genotyping Hepatitis B virus by Next-Generation Sequencing: Detection of Mixed Infections and Analysis of Sequence Conservation. Int J Mol Sci 2024; 25:5481. [PMID: 38791519 PMCID: PMC11122360 DOI: 10.3390/ijms25105481] [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: 03/29/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5' end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A-H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies.
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Affiliation(s)
- Eva Dopico
- Department of Microbiology, Metropolitana Sud Territorial Clinical Laboratory, Bellvitge University Hospital, Institut Català de la Salut (ICS), 08907 Hospitalet de Llobregat, Spain; (E.D.); (L.G.); (I.U.)
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain
| | - Marta Vila
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
| | - David Tabernero
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
| | - Ariadna Rando-Segura
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Virology Section, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.G.-S.); (A.A.); (T.P.)
| | - Beatriz Pacín-Ruíz
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
| | - Laura Guerrero
- Department of Microbiology, Metropolitana Sud Territorial Clinical Laboratory, Bellvitge University Hospital, Institut Català de la Salut (ICS), 08907 Hospitalet de Llobregat, Spain; (E.D.); (L.G.); (I.U.)
| | - Itziar Ubillos
- Department of Microbiology, Metropolitana Sud Territorial Clinical Laboratory, Bellvitge University Hospital, Institut Català de la Salut (ICS), 08907 Hospitalet de Llobregat, Spain; (E.D.); (L.G.); (I.U.)
| | - Miguel J. Martínez
- Department of Microbiology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (M.J.M.); (J.C.)
- ISGlobal, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Josep Costa
- Department of Microbiology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (M.J.M.); (J.C.)
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Javier Pérez-Garreta
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
| | - Alejandra González-Sánchez
- Virology Section, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.G.-S.); (A.A.); (T.P.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Respiratory Virus Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Andrés Antón
- Virology Section, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.G.-S.); (A.A.); (T.P.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Respiratory Virus Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Tomás Pumarola
- Virology Section, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.G.-S.); (A.A.); (T.P.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Liver Unit, Internal Medicine Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Roser Ferrer-Costa
- Clinical Biochemistry, Drug Delivery and Therapy (CB-DDT) Research Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
- Biochemistry Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Liver Unit, Internal Medicine Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Clinical Biochemistry, Drug Delivery and Therapy (CB-DDT) Research Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
- Department of Basic Sciences, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - Maria Francesca Cortese
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
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Kalirad A, Burch CL, Azevedo RBR. Genetic drift promotes and recombination hinders speciation on holey fitness landscapes. PLoS Genet 2024; 20:e1011126. [PMID: 38252672 PMCID: PMC10833538 DOI: 10.1371/journal.pgen.1011126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 02/01/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Dobzhansky and Muller proposed a general mechanism through which microevolution, the substitution of alleles within populations, can cause the evolution of reproductive isolation between populations and, therefore, macroevolution. As allopatric populations diverge, many combinations of alleles differing between them have not been tested by natural selection and may thus be incompatible. Such genetic incompatibilities often cause low fitness in hybrids between species. Furthermore, the number of incompatibilities grows with the genetic distance between diverging populations. However, what determines the rate and pattern of accumulation of incompatibilities remains unclear. We investigate this question by simulating evolution on holey fitness landscapes on which genetic incompatibilities can be identified unambiguously. We find that genetic incompatibilities accumulate more slowly among genetically robust populations and identify two determinants of the accumulation rate: recombination rate and population size. In large populations with abundant genetic variation, recombination selects for increased genetic robustness and, consequently, incompatibilities accumulate more slowly. In small populations, genetic drift interferes with this process and promotes the accumulation of genetic incompatibilities. Our results suggest a novel mechanism by which genetic drift promotes and recombination hinders speciation.
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Affiliation(s)
- Ata Kalirad
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Christina L. Burch
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ricardo B. R. Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
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3
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Cremer J, van Heiningen F, Veldhuijzen I, Benschop K. Characterization of Hepatitis B virus based complete genome analysis improves molecular surveillance and enables identification of a recombinant C/D strain in the Netherlands. Heliyon 2023; 9:e22358. [PMID: 38058647 PMCID: PMC10695994 DOI: 10.1016/j.heliyon.2023.e22358] [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: 08/18/2023] [Revised: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Hepatitis B Virus (HBV) is classified into 10 HBV genotypes (A-J) based a >7.5 % divergence within the complete genome or a >4 % divergence in the S-gene. In addition, recombinant strains with common breakpoints at the gene boundaries of the preS1/preS2/S- and preC/C-gene are often identified. Analysis of HBV based on the complete genome is essential for public health surveillance as it provides higher genetic resolution to conduct accurate characterization and phylogenetic analysis of circulating strains and identify possible recombinants. Currently two separate assays are used for HBV-surveillance; the S-gene for typing, and due to the higher genetic variation, the C-gene to gain insight in transmission patterns. The aim of the study was to develop a complete genome PCR-assay and evaluate the characterization and circulation of HBV strains through the use of the S-gene, C-gene and complete genome. For this HBV positive samples collected in the period 2017 through 2019 were selected. Analysis of the complete genome showed that complete genome analysis portrays a high genetic resolution that provided accurate characterization and analysis of the different circulating types in the Netherlands and enabled identification and characterization of a recombinant CD strain.
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Affiliation(s)
- Jeroen Cremer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Francoise van Heiningen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Irene Veldhuijzen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Kimberley Benschop
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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Jose-Abrego A, Roman S, Laguna-Meraz S, Panduro A. Host and HBV Interactions and Their Potential Impact on Clinical Outcomes. Pathogens 2023; 12:1146. [PMID: 37764954 PMCID: PMC10535809 DOI: 10.3390/pathogens12091146] [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: 08/09/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Hepatitis B virus (HBV) is a challenge for global health services, affecting millions and leading thousands to end-stage liver disease each year. This comprehensive review explores the interactions between HBV and the host, examining their impact on clinical outcomes. HBV infection encompasses a spectrum of severity, ranging from acute hepatitis B to chronic hepatitis B, which can potentially progress to cirrhosis and hepatocellular carcinoma (HCC). Occult hepatitis B infection (OBI), characterized by low HBV DNA levels in hepatitis B surface antigen-negative individuals, can reactivate and cause acute hepatitis B. HBV genotyping has revealed unique geographical patterns and relationships with clinical outcomes. Moreover, single nucleotide polymorphisms (SNPs) within the human host genome have been linked to several clinical outcomes, including cirrhosis, HCC, OBI, hepatitis B reactivation, and spontaneous clearance. The immune response plays a key role in controlling HBV infection by eliminating infected cells and neutralizing HBV in the bloodstream. Furthermore, HBV can modulate host metabolic pathways involved in glucose and lipid metabolism and bile acid absorption, influencing disease progression. HBV clinical outcomes correlate with three levels of viral adaptation. In conclusion, the clinical outcomes of HBV infection could result from complex immune and metabolic interactions between the host and HBV. These outcomes can vary among populations and are influenced by HBV genotypes, host genetics, environmental factors, and lifestyle. Understanding the degrees of HBV adaptation is essential for developing region-specific control and prevention measures.
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Affiliation(s)
- Alexis Jose-Abrego
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (A.J.-A.); (S.R.); (S.L.-M.)
- Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (A.J.-A.); (S.R.); (S.L.-M.)
- Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Saul Laguna-Meraz
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (A.J.-A.); (S.R.); (S.L.-M.)
- Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Arturo Panduro
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (A.J.-A.); (S.R.); (S.L.-M.)
- Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
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Marchio A, Sitbounlang P, Deharo E, Paboriboune P, Pineau P. Concealed for a Long Time on the Marches of Empires: Hepatitis B Virus Genotype I. Microorganisms 2023; 11:2204. [PMID: 37764048 PMCID: PMC10535388 DOI: 10.3390/microorganisms11092204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/18/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Genotype I, the penultimate HBV genotype to date, was granted the status of a bona fide genotype only in the XXIst century after some hesitations. The reason for these hesitations was that genotype I is a complex recombinant virus formed with segments from three original genotypes, A, C, and G. It was estimated that genotype I is responsible for only an infinitesimal fraction (<1.0%) of the chronic HBV infection burden worldwide. Furthermore, most probably due to its recent discovery and rarity, the natural history of infection with genotype I is poorly known in comparison with those of genotypes B or C that predominate in their area of circulation. Overall, genotype I is a minor genotype infecting ethnic minorities. It is endemic to the Southeast Asian Massif or Eastern Zomia, a vast mountainous or hilly region of 2.5 million km2 spreading from Eastern India to China, inhabited by a little more than 100 million persons belonging primarily to ethnic minorities speaking various types of languages (Tibeto-Burman, Austroasiatic, and Tai-Kadai) who managed to escape the authority of central states during historical times. Genotype I consists of two subtypes: I1, present in China, Laos, Thailand, and Vietnam; and I2, encountered in India, Laos, and Vietnam.
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Affiliation(s)
- Agnès Marchio
- Institut Pasteur, Université Paris Cité, Unité “Organisation Nucléaire et Oncogenèse”, INSERM U993, 75015 Paris, France;
| | - Philavanh Sitbounlang
- Centre d’Infectiologie Lao-Christophe Mérieux (CILM), Vientiane 3888, Laos; (P.S.); (P.P.)
| | - Eric Deharo
- MIVEGEC, Université Montpellier, CNRS, IRD, 34394 Montpellier, France;
| | - Phimpha Paboriboune
- Centre d’Infectiologie Lao-Christophe Mérieux (CILM), Vientiane 3888, Laos; (P.S.); (P.P.)
| | - Pascal Pineau
- Institut Pasteur, Université Paris Cité, Unité “Organisation Nucléaire et Oncogenèse”, INSERM U993, 75015 Paris, France;
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Toyé RM, Loureiro CL, Jaspe RC, Zoulim F, Pujol FH, Chemin I. The Hepatitis B Virus Genotypes E to J: The Overlooked Genotypes. Microorganisms 2023; 11:1908. [PMID: 37630468 PMCID: PMC10459053 DOI: 10.3390/microorganisms11081908] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Hepatitis B virus (HBV) genotypes E to J are understudied genotypes. Genotype E is found almost exclusively in West Africa. Genotypes F and H are found in America and are rare in other parts of the world. The distribution of genotype G is not completely known. Genotypes I and J are found in Asia and probably result from recombination events with other genotypes. The number of reported sequences for HBV genotypes E to J is small compared to other genotypes, which could impact phylogenetic and pairwise distance analyses. Genotype F is the most divergent of the HBV genotypes and is subdivided into six subgenotypes F1 to F6. Genotype E may be a recent genotype circulating almost exclusively in sub-Saharan Africa. Genotype J is a putative genotype originating from a single Japanese patient. The paucity of data from sub-Saharan Africa and Latin America is due to the under-representation of these regions in clinical and research cohorts. The purpose of this review is to highlight the need for further research on HBV genotypes E to J, which appear to be overlooked genotypes.
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Affiliation(s)
- Rayana Maryse Toyé
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1052, Centre de Recherche en Cancérologie de Lyon (CRCL), 151 Cours Albert Thomas, 69003 Lyon, France; (R.M.T.); (F.Z.)
| | - Carmen Luisa Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela; (C.L.L.); (R.C.J.)
| | - Rossana Celeste Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela; (C.L.L.); (R.C.J.)
| | - Fabien Zoulim
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1052, Centre de Recherche en Cancérologie de Lyon (CRCL), 151 Cours Albert Thomas, 69003 Lyon, France; (R.M.T.); (F.Z.)
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular (CMBC), Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela; (C.L.L.); (R.C.J.)
- Collégium de Lyon, Institut d’Etudes Avancées, Université Lyon 2, 69007 Lyon, France
| | - Isabelle Chemin
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1052, Centre de Recherche en Cancérologie de Lyon (CRCL), 151 Cours Albert Thomas, 69003 Lyon, France; (R.M.T.); (F.Z.)
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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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Xu S, Mu X, Xu X, Bi C, Ji J, Kan Y, Yao L, Bi Y, Xie Q. Genetic Heterogeneity and Mutated PreS Analysis of Duck Hepatitis B Virus Recently Isolated from Ducks and Geese in China. Animals (Basel) 2023; 13:ani13081282. [PMID: 37106845 PMCID: PMC10135025 DOI: 10.3390/ani13081282] [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: 02/23/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, we detected 12 duck and 11 goose flocks that were positive for duck hepatitis B virus (DHBV) using polymerase chain reaction and isolated 23 strains between 2020 and 2022 in China. The complete genomes of goose strains E200801 and E210501 shared the highest identity (99.9%), whereas those of strains Y220217 and E210526 shared the lowest identity (91.39%). The phylogenetic tree constructed based on the genome sequences of these strains and reference strains was classified into three major clusters: the Chinese branch DHBV-I, the Chinese branch DHBV-II, and the Western branch DHBV-III. Furthermore, the duck-origin strain Y200122 was clustered into a separate branch and was predicted to be a recombinant strain derived from DHBV-M32990 (belonging to the Chinese branch DHBV-I) and Y220201 (belonging to the Chinese branch DHBV-II). Additionally, preS protein analysis of the 23 DHBV strains revealed extensive mutation sites, almost half of which were of duck origin. All goose-origin DHBV contained the mutation site G133E, which is related to increased viral pathogenicity. These data are expected to promote further research on the epidemiology and evolution of DHBV. Continuing DHBV surveillance in poultry will enhance the understanding of the evolution of HBV.
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Affiliation(s)
- Shuqi Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Xinhao Mu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Congying Bi
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, China
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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9
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Bello KE, Mat Jusoh TNA, Irekeola AA, Abu N, Mohd Amin NAZ, Mustaffa N, Shueb RH. A Recent Prevalence of Hepatitis B Virus (HBV) Genotypes and Subtypes in Asia: A Systematic Review and Meta-Analysis. Healthcare (Basel) 2023; 11:healthcare11071011. [PMID: 37046937 PMCID: PMC10094200 DOI: 10.3390/healthcare11071011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
Background and Aim: Despite introducing the hepatitis B virus (HBV) vaccine, the incidence of the Hepatitis B virus globally is still a major health concern. This systematic review and meta-analysis were conducted to provide detailed information on the prevalence of HBV genotypes and subtypes in circulation in Asia. Methods: A systematic search for articles describing the prevalence of HBV genotypes and subtypes in Asia was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines. Results: Our search returned 207 eligible articles involving 49,279 genotypes and 7457 subtypes representing 28 Asian countries. A meta-analysis was performed on our eligible studies using the Random effect Model. The pooled prevalence of HBV genotypes showed that genotype C (30.9%) (95% CI, 27.5–34.5%; I2 = 97.57%; p < 0.001) was the most common HBV genotype in Asia, followed by genotype B (17.8%) (95% CI, 15.5–20.4%; I2 = 97.26%; p < 0.001) and genotype D (15.4%) (95% CI, 11.8–19.8%). Vietnam had the highest prevalence of genotype B, Lebanon had the highest prevalence of genotypes C, and Jordan had the highest prevalence of genotype D. There was variation in genotypic prevalence with respect to the target genes for HBV genotyping. Reverse dot blot hybridization had the highest estimate of genotypes B and C. HBV subtype C2 (40.0%) (95% CI, 33.3–47.0) is the most prevalent HBV subtype. Conclusion: Evidence from this study reveals that HBV genotypes C and B are the most dominant HBV genotypes in Asia, and HBV subtype C2 is more endemic in Asia.
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Affiliation(s)
- Kizito Eneye Bello
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Microbiology, Faculty of Natural Science, Kogi State University (Prince Abubakar Audu University), Anyigba 1008, Kogi State, Nigeria
| | - Tuan Nur Akmalina Mat Jusoh
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, Offa 4412, Kwara State, Nigeria
| | - Norhidayah Abu
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Advanced Materials Research Centre (A.M.R.E.C.), Lot 34 Jalan Hi-Tech 2/3, Kulim Hi-Tech Park, Kulim 09000, Kedah, Malaysia
| | - Nur Amalin Zahirah Mohd Amin
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nazri Mustaffa
- Department of Medicine, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Rafidah Hanim Shueb
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Institute for Research in Molecular Medicine (I.N.F.O.R.M.M.), Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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10
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Youssef DM, El-Shal AS, Elbehidy RM, Fouda MA, Shalaby SM, El Hawy LL, Elsadek AF, Neemat-Allah MAA, Ramadan SM, Gohary A, Arab F, Alsharkawy M, Tolba SAR, Abdelsalam MM, Amin EK, Gehad MH. Hepatitis B Immunization Status in Children with Chronic Kidney Disease: Experience at a Single Center, Egypt. J Clin Med 2023; 12:jcm12051864. [PMID: 36902652 PMCID: PMC10003117 DOI: 10.3390/jcm12051864] [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: 07/16/2022] [Revised: 08/16/2022] [Accepted: 08/21/2022] [Indexed: 03/03/2023] Open
Abstract
Background: Children with chronic kidney disease (CKD), particularly those who require hemodialysis (HD), are at high risk of hepatitis B virus (HBV) infection. The HBV vaccine non-/hypo-response rate among HD children remains high, and it is critical to investigate the influencing factors and their linkages. The aim of this study was to identify the pattern of HB vaccination response in HD children and to analyze the interference of various clinical and biomedical factors with the immunological response to HB vaccination. Methods: This cross-sectional study included 74 children on maintenance hemodialysis, aged between 3 and 18 years. These children were subjected to complete clinical examination and laboratory investigations. Results: Out of a total of 74 children with HD, 25 (33.8%) were positive for the HCV antibody. Regarding the immunological response to hepatitis B vaccine, 70% were non-/hypo-responders (≤100 IU/mL) and only 30% mounted a high-level response (more than 100 IU/mL). There was a significant relation between non-/hypo-response and sex, dialysis duration, and HCV infection. Being on dialysis for more than 5 years and being HCV Ab-positive were independent variables for non-/hypo-response to HB vaccine. Conclusions: Children with CKD on regular HD have poor seroconversion rates in response to the HBV vaccine, which were influenced by dialysis duration and HCV infection.
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Affiliation(s)
- Doaa Mohammed Youssef
- Pediatrics Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Amal S. El-Shal
- Medical Biochemistry Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
- Medical Biochemistry and Molecular Biology Department, Armed Forces College of Medicine (AFCM), Cairo 11774, Egypt
- Correspondence: or ; Tel.: +20-1221546634
| | - Rabab M. Elbehidy
- Pediatrics Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Mohamed Adel Fouda
- Public Health and Community Medicine, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Sally M. Shalaby
- Medical Biochemistry Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Lamiaa Lotfy El Hawy
- Public Health and Community Medicine, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt
| | | | | | - Seham M. Ramadan
- Pediatrics Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Amal Gohary
- Pediatrics Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Faika Arab
- Pediatrics Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Mona Alsharkawy
- Pediatrics Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
| | | | | | - Ezzat Kamel Amin
- Pediatrics Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Mona Hamed Gehad
- Pediatrics Department, Faculty of Human Medicine, Zagazig University, Zagazig 44519, Egypt
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11
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A novel subgenotype I3 of hepatitis B virus in Guangxi, China: a 15-year follow-up study. Virus Genes 2023; 59:359-369. [PMID: 36841897 DOI: 10.1007/s11262-023-01980-6] [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: 10/21/2022] [Accepted: 02/13/2023] [Indexed: 02/27/2023]
Abstract
Genotype I of hepatitis B virus (HBV) was proposed recently following sequencing of complete HBV genomes from Vietnam and Laos. However, its long-term molecular evolution is unknown. The objectives of this study were to study the molecular evolution of this genotype from an asymptomatic HBsAg carrier from the Long An cohort over a 15-year period was studied using both NGS and clone-based sequencing. The number of complete genome sequences obtained in 2004, 2007, 2013, and 2019 are 17, 20, 19, and 10, respectively. All strains belong to subgenotype I1, except for six (five from 2007 and one from 2019) and 8 further strains from 2007 which form a cluster branching out from other subgenotype I sequences, supported by a 100% bootstrap value. Based on complete genome sequences, all of the estimated intragroup nucleotide divergence values between these strains and HBV subgenotypes I1-I2 exceed 4%. These strains are recombinants between genotype I1 and subgenotype C but the breakpoints vary. The median intrahost viral evolutionary rate in this carrier was 3.88E-4 substitutions per site per year. The Shannon entropy (Sn) ranged from 0.55 to 0.88 and the genetic diversity, D, ranged from 0.0022 to 0.0041. In conclusion, our data provide evidence of novel subgenotypes. Considering that the 8 strains disappeared after 2007, while one of the 6 strains appears again in 2019, we propose these 6 strains as a new subgenotype, provisionally designated HBV subgenotype I3 and the 8 strains as aberrant genotype.
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12
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Lourenço J, McNaughton AL, Pley C, Obolski U, Gupta S, Matthews PC. Polymorphisms predicting phylogeny in hepatitis B virus. Virus Evol 2022; 9:veac116. [PMID: 36628296 PMCID: PMC9825179 DOI: 10.1093/ve/veac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/30/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B viruses (HBVs) are compact viruses with circular genomes of ∼3.2 kb in length. Four genes (HBx, Core, Surface, and Polymerase) generating seven products are encoded on overlapping reading frames. Ten HBV genotypes have been characterised (A-J), which may account for differences in transmission, outcomes of infection, and treatment response. However, HBV genotyping is rarely undertaken, and sequencing remains inaccessible in many settings. We set out to assess which amino acid (aa) sites in the HBV genome are most informative for determining genotype, using a machine learning approach based on random forest algorithms (RFA). We downloaded 5,496 genome-length HBV sequences from a public database, excluding recombinant sequences, regions with conserved indels, and genotypes I and J. Each gene was separately translated into aa, and the proteins concatenated into a single sequence (length 1,614 aa). Using RFA, we searched for aa sites predictive of genotype and assessed covariation among the sites with a mutual information-based method. We were able to discriminate confidently between genotypes A-H using ten aa sites. Half of these sites (5/10) sites were identified in Polymerase (Pol), of which 4/5 were in the spacer domain and one in reverse transcriptase. A further 4/10 sites were located in Surface protein and a single site in HBx. There were no informative sites in Core. Properties of the aa were generally not conserved between genotypes at informative sites. Among the highest co-varying pairs of sites, there were fifty-five pairs that included one of these 'top ten' sites. Overall, we have shown that RFA analysis is a powerful tool for identifying aa sites that predict the HBV lineage, with an unexpectedly high number of such sites in the spacer domain, which has conventionally been viewed as unimportant for structure or function. Our results improve ease of genotype prediction from limited regions of HBV sequences and may have future applications in understanding HBV evolution.
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Affiliation(s)
| | | | - Caitlin Pley
- Guy’s and St Thomas’ NHS Foundation Trust, Westminster Bridge Rd, London SE1 7EH, UK
| | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv 6997801, Israel,Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
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13
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Váradi A, Kaszab E, Kardos G, Prépost E, Szarka K, Laczkó L. Rapid genotyping of targeted viral samples using Illumina short-read sequencing data. PLoS One 2022; 17:e0274414. [PMID: 36112576 PMCID: PMC9481040 DOI: 10.1371/journal.pone.0274414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/30/2022] [Indexed: 11/19/2022] Open
Abstract
The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the project’s GitHub page (https://github.com/laczkol/QVG).
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Affiliation(s)
- Alex Váradi
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- Department of Laboratory Medicine, University of Pécs, Pécs, Hungary
| | - Eszter Kaszab
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Gábor Kardos
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Eszter Prépost
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Krisztina Szarka
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Levente Laczkó
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- ELKH-DE Conservation Biology Research Group, Debrecen, Hungary
- * E-mail:
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14
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Pacholi S, Bishwal SC, Barde PV. Identification of hepatitis B virus genotypes detected in Lahaul & Spiti district of Himachal Pradesh, India. Indian J Med Res 2022; 156:779-785. [PMID: 37056078 DOI: 10.4103/ijmr.ijmr_442_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
Background & objectives Infection by hepatitis B virus (HBV) results in acute or chronic hepatitis. Based on sequence differences of eight per cent or more, HBV is divided into 10 genotypes (A to J) and 35 sub-genotypes. Molecular characterization of the circulating HBV genome has helped in understanding the epidemiology and its clinical importance. Spiti valley in Himachal Pradesh, which shares its border with Tibet, is one of the most HBV prevalent areas in India. Since information about the circulating genotype/s of HBV in this area is limited, this study was conducted to identify the circulating HBV genotypes. Methods The surface and partial reverse transcriptase gene regions were sequenced using 14 hepatitis B surface antigen-positive samples. Results Out of the 14 hepatitis B surface antigen-positive samples 11 sample gave quality sequence for further analysis. All the 11 samples belonged to subtype ayw2. The phylogenetic and recombination analysis revealed that five out of 11 samples were of genotype CD1 and the rest six were of genotype D3. Interpretation & conclusions The CD1 recombinant sub-genotype might have immigrated during past or present transcontinental migration between the adjacent countries. Further studies using full-genome sequencing and high sample size will be helpful to understand this epidemiology and to combat the high prevalence of HBV in the area.
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Affiliation(s)
- Sanchita Pacholi
- Division of Virology & Zoonoses, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Subasa Chandra Bishwal
- Division of Virology & Zoonoses, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Pradip V Barde
- Division of Virology & Zoonoses, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
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15
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Chen QY, Jia HH, Wang XY, Shi YL, Zhang LJ, Hu LP, Wang C, He X, Harrison TJ, Jackson JB, Wu L, Fang ZL. Analysis of entire hepatitis B virus genomes reveals reversion of mutations to wild type in natural infection, a 15 year follow-up study. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105184. [PMID: 34902556 DOI: 10.1016/j.meegid.2021.105184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
It has been reported that some mutations in the genome of hepatitis B virus (HBV) may predict the outcome of the virus infection. However, evolutionary data derived from long-term longitudinal analysis of entire HBV genomes using next generation sequencing (NGS) remain rare. In this study, serum samples were collected from asymptomatic hepatitis B surface antigen (HBsAg) carriers from a long-term prospective cohort. The entire HBV genome was amplified by polymerase chain reaction (PCR) and sequenced using NGS. Twenty-eight time series serum samples from nine subjects were successfully analysed. The Shannon entropy (Sn) ranged from 0 to 0.89, with a median value of 0.76, and the genetic diversity (D) ranged from 0 to 0.013, with a median value of 0.004. Intrahost HBV viral evolutionary rates ranged from 2.39E-04 to 3.11E-03. Double mutations at nt1762(A → T) and 1764(G → A) and a stop mutation at nt1896(G → A) were seen in all sequences from subject BO129 in 2007. However, in 2019, most sequences were wild type at these positions. Deletions between nt 2920-3040 were seen in all sequences from subject TS115 in 2007 and 2013 but these were not present in 2004 or 2019. Some sequences from subject CC246 had predicted escape substitutions (T123N, G145R) in the surface protein in 2004, 2013 and 2019 but none of the sequences from 2007 had these changes. In conclusion, HBV mutations may revert to wild type in natural infection. Clinicians should be wary of predicting long-term prognoses on the basis of the presence of mutations.
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Affiliation(s)
- Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Hui-Hua Jia
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China; School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Yun-Liang Shi
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Lu-Juan Zhang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Li-Ping Hu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Chao Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Xiang He
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
| | - Tim J Harrison
- Division of Medicine, University College London Medical School, London, UK
| | - J Brooks Jackson
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China.
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16
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Ingasia LAO, Wose Kinge C, Kramvis A. Genotype E: The neglected genotype of hepatitis B virus. World J Hepatol 2021; 13:1875-1891. [PMID: 35069995 PMCID: PMC8727212 DOI: 10.4254/wjh.v13.i12.1875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/15/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) (sub)genotypes A1, D3 and E circulate in sub-Saharan Africa, the region with one of the highest incidences of HBV-associated hepatocellular carcinoma globally. Although genotype E was identified more than 20 years ago, and is the most widespread genotype in Africa, it has not been extensively studied. The current knowledge status and gaps in its origin and evolution, natural history of infection, disease progression, response to antiviral therapy and vaccination are discussed. Genotype E is an African genotype, with unique molecular characteristics that is found mainly in Western and Central Africa and rarely outside Africa except in individuals of African descent. The low prevalence of this genotype in the African descendant populations in the New World, phylogeographic analyses, the low genetic diversity and evidence of remnants of genotype E in ancient HBV samples suggests the relatively recent re-introduction into the population. There is scarcity of information on the clinical and virological characteristics of genotype E-infected patients, disease progression and outcomes and efficacy of anti-HBV drugs. Individuals infected with genotype E have been characterised with high hepatitis B e antigen-positivity and high viral load with a lower end of treatment response to interferon-alpha. A minority of genotype E-infected participants have been included in studies in which treatment response was monitored. Of concern is that current guidelines do not consider patients infected with genotype E. Thus, there is an urgent need for further large-scale investigations into genotype E, the neglected genotype of HBV.
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Affiliation(s)
- Luicer Anne Olubayo Ingasia
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, Gauteng, South Africa
| | - Constance Wose Kinge
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, Gauteng, South Africa
- Department of Implementation Science, Right to Care, Johannesburg 0046, Gauteng, South Africa
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, Gauteng, South Africa
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17
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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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18
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Ghosh S, Chakraborty A, Banerjee S. Persistence of Hepatitis B Virus Infection: A Multi-Faceted Player for Hepatocarcinogenesis. Front Microbiol 2021; 12:678537. [PMID: 34526974 PMCID: PMC8435854 DOI: 10.3389/fmicb.2021.678537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) infection has a multi-dimensional effect on the host, which not only alters the dynamics of immune response but also persists in the hepatocytes to predispose oncogenic factors. The virus exists in multiple forms of which the nuclear localized covalently closed circular DNA (cccDNA) is the most stable and the primary reason for viral persistence even after clearance of surface antigen and viral DNA. The second reason is the existence of pregenomic RNA (pgRNA) containing virion particles. On the other hand, the integration of the viral genome in the host chromosome also leads to persistent production of viral proteins along with the chromosomal instabilities. The interferon treatment or administration of nucleot(s)ide analogs leads to reduction in the viral DNA load, but the pgRNA and surface antigen clearance are a slow process and complete loss of serological HBsAg is rare. The prolonged exposure of immune cells to the viral antigens, particularly HBs antigen, in the blood circulation results in T-cell exhaustion, which disrupts immune clearance of the virus and virus-infected cells. In addition, it predisposes immune-tolerant microenvironment, which facilitates the tumor progression. Thus cccDNA, pgRNA, and HBsAg along with the viral DNA could be the therapeutic targets in the early disease stages that may improve the quality of life of chronic hepatitis B patients by impeding the progression of the disease toward hepatocellular carcinoma.
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Affiliation(s)
| | | | - Soma Banerjee
- Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India
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19
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Ou G, He L, Wang L, Song J, Lai X, Tian X, Wang L, Zhang K, Zhang X, Deng J, Zhuang H, Xiang K, Li T. The Genotype (A to H) Dependent N-terminal Sequence of HBV Large Surface Protein Affects Viral Replication, Secretion and Infectivity. Front Microbiol 2021; 12:687785. [PMID: 34305848 PMCID: PMC8299529 DOI: 10.3389/fmicb.2021.687785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
Genetic variability has significant impacts on biological characteristics and pathogenicity of hepatitis B virus (HBV), in which the N-terminal sequence of the presurface 1 (preS1) region of HBV large surface protein (LHBs) displays genotype (GT) dependent genetic heterogeneity. However, the influence of this heterogeneity on its biological roles is largely unknown. By analyzing 6560 full-length genome sequences of GTA-GTH downloaded from HBVdb database, the preS1 N-terminal sequences were divided into four representative types, namely C-type (representative of GTA, GTB, and GTC), H-type (GTF and GTH), E-type (GTE and GTG), and D-type (GTD), respectively. We artificially substituted the preS1 N-termini of GTC and GTD plasmids or viral strains with each sequence of the four representative types. The roles of preS1 N-terminus on HBV replication, secretion and infectivity were investigated using HepG2 or HepG2-NTCP cells. In the transfection experiments, the results showed that the extracellular HBsAg levels and HBsAg secretion coefficients in D- and E-type strains were significantly higher than those in C- and H-type strains. D-type strain produced more extracellular HBV DNA than C-type strain. We further observed that D-, H-, and E-type strains increased the levels of intracellular replicative HBV DNAs, comparing with C-type strain. In the infection experiments, the levels of extracellular HBeAg, intracellular HBV total RNA and pgRNA/preC mRNA in D- and E-type strains were markedly higher than C and H-type ones. Our data suggest that the preS1 N-termini affect HBV replication, secretion and infectivity in a genotype dependent manner. The C- and H-type strains prefer to attenuate HBsAg secretion, while the strains of D- and E-type promoted infectivity. The existence and function of the intergenotypic shift of preS1 in naturally occurring recombination requires further investigation, as the data we acquired are mostly related to recombinant preS1 region between N-terminus of preS1 from genotypes A-H and the remaining preS1 portion of GTC or GTD.
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Affiliation(s)
- Guomin Ou
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lingyuan He
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Luwei Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Department of Clinical Laboratory Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Ji Song
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xinyuan Lai
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xing Tian
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lei Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Kai Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xuechao Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Juan Deng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hui Zhuang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Kuanhui Xiang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Tong Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
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20
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Modular Evolution of Coronavirus Genomes. Viruses 2021; 13:v13071270. [PMID: 34209881 PMCID: PMC8310335 DOI: 10.3390/v13071270] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic compatibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. In contrast, avian gammacoronaviruses recombined extensively and exist as a global cloud of genes with poorly corresponding genetic distances in different parts of the genome. Spike, but not other structural proteins, was most commonly exchanged between coronaviruses. Recombination patterns differed between coronavirus genera and corresponded to the modular structure of the spike: recombination traces were more pronounced between spike domains (N-terminal and C-terminal parts of S1 and S2) than within domains. The variability of possible recombination events and their uneven distribution over the genome suggest that compatibility of genes, rather than mechanistic or ecological limitations, shapes recombination patterns in coronaviruses.
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21
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Locarnini SA, Littlejohn M, Yuen LKW. Origins and Evolution of the Primate Hepatitis B Virus. Front Microbiol 2021; 12:653684. [PMID: 34108947 PMCID: PMC8180572 DOI: 10.3389/fmicb.2021.653684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
Recent interest in the origins and subsequent evolution of the hepatitis B virus (HBV) has strengthened with the discovery of ancient HBV sequences in fossilized remains of humans dating back to the Neolithic period around 7,000 years ago. Metagenomic analysis identified a number of African non-human primate HBV sequences in the oldest samples collected, indicating that human HBV may have at some stage, evolved in Africa following zoonotic transmissions from higher primates. Ancestral genotype A and D isolates were also discovered from the Bronze Age, not in Africa but rather Eurasia, implying a more complex evolutionary and migratory history for HBV than previously recognized. Most full-length ancient HBV sequences exhibited features of inter genotypic recombination, confirming the importance of recombination and the mutation rate of the error-prone viral replicase as drivers for successful HBV evolution. A model for the origin and evolution of HBV is proposed, which includes multiple cross-species transmissions and favors subsequent recombination events that result in a pathogen and can successfully transmit and cause persistent infection in the primate host.
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Affiliation(s)
- Stephen A Locarnini
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Lilly K W Yuen
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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22
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Abstract
Viral recombination is a major evolutionary mechanism driving adaptation processes, such as the ability of host-switching. Understanding global patterns of recombination could help to identify underlying mechanisms and to evaluate the potential risks of rapid adaptation. Conventional approaches (e.g., those based on linkage disequilibrium) are computationally demanding or even intractable when sequence alignments include hundreds of sequences, common in viral data sets. We present a comprehensive analysis of recombination across 30 genomic alignments from viruses infecting humans. In order to scale the analysis and avoid the computational limitations of conventional approaches, we apply newly developed topological data analysis methods able to infer recombination rates for large data sets. We show that viruses, such as ZEBOV and MARV, consistently displayed low levels of recombination, whereas high levels of recombination were observed in Sarbecoviruses, HBV, HEV, Rhinovirus A, and HIV. We observe that recombination is more common in positive single-stranded RNA viruses than in negatively single-stranded RNA ones. Interestingly, the comparison across multiple viruses suggests an inverse correlation between genome length and recombination rate. Positional analyses of recombination breakpoints along viral genomes, combined with our approach, detected at least 39 nonuniform patterns of recombination (i.e., cold or hotspots) in 18 viral groups. Among these, noteworthy hotspots are found in MERS-CoV and Sarbecoviruses (at spike, Nucleocapsid and ORF8). In summary, we have developed a fast pipeline to measure recombination that, combined with other approaches, has allowed us to find both common and lineage-specific patterns of recombination among viruses with potential relevance in viral adaptation.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Ioan Filip
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
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23
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Cagliani R, Mozzi A, Pontremoli C, Sironi M. Evolution and Origin of Human Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Kutnjak D, Tamisier L, Adams I, Boonham N, Candresse T, Chiumenti M, De Jonghe K, Kreuze JF, Lefebvre M, Silva G, Malapi-Wight M, Margaria P, Mavrič Pleško I, McGreig S, Miozzi L, Remenant B, Reynard JS, Rollin J, Rott M, Schumpp O, Massart S, Haegeman A. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms 2021; 9:841. [PMID: 33920047 PMCID: PMC8071028 DOI: 10.3390/microorganisms9040841] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.
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Affiliation(s)
- Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Lucie Tamisier
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Ian Adams
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Neil Boonham
- Institute for Agri-Food Research and Innovation, Newcastle University, King’s Rd, Newcastle Upon Tyne NE1 7RU, UK;
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, National Research Council, Via Amendola, 122/D, 70126 Bari, Italy;
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
| | - Jan F. Kreuze
- International Potato Center (CIP), Avenida la Molina 1895, La Molina, Lima 15023, Peru;
| | - Marie Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK;
| | - Martha Malapi-Wight
- Biotechnology Risk Analysis Programs, Biotechnology Regulatory Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Riverdale, MD 20737, USA;
| | - Paolo Margaria
- Leibniz Institute-DSMZ, Inhoffenstrasse 7b, 38124 Braunschweig, Germany;
| | - Irena Mavrič Pleško
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia;
| | - Sam McGreig
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy;
| | - Benoit Remenant
- ANSES Plant Health Laboratory, 7 Rue Jean Dixméras, CEDEX 01, 49044 Angers, France;
| | | | - Johan Rollin
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
- DNAVision, 6041 Charleroi, Belgium
| | - Mike Rott
- Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada;
| | - Olivier Schumpp
- Agroscope, Route de Duillier 50, 1260 Nyon, Switzerland; (J.-S.R.); (O.S.)
| | - Sébastien Massart
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
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25
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Jose-Abrego A, Roman S, Rebello Pinho JR, de Castro VFD, Panduro A. Hepatitis B Virus (HBV) Genotype Mixtures, Viral Load, and Liver Damage in HBV Patients Co-infected With Human Immunodeficiency Virus. Front Microbiol 2021; 12:640889. [PMID: 33746932 PMCID: PMC7966718 DOI: 10.3389/fmicb.2021.640889] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/10/2021] [Indexed: 01/11/2023] Open
Abstract
Hepatitis B virus (HBV) co-infection is possible in patients who are positive for human immunodeficiency virus (HIV) since both share similar transmission routes. Furthermore, through the continuous risk of exposure, they potentially can be infected by mixtures of distinct HBV genotypes which can result in the presence of two or more genotypes in a single patient. This study aimed to specify the frequency of mixtures of HBV genotypes and their potential clinic importance in HIV-infected Mexican patients. HBV infection was assessed by serological testing and molecular diagnostics. HBV mixtures were detected by multiplex PCR and DNA sequencing. Liver fibrosis was evaluated using transitional elastography, the Aspartate aminotransferase to Platelets Ratio Index score, and Fibrosis-4 score. Among 228 HIV-infected patients, 67 were positive for HBsAg. In 25 HBV/HIV co-infected patients, 44 HBV genotypes were found: H (50.0%, 22/44), G (22.7%, 10/44), D (15.9%, 6/44), A (9.1%, 4/44), and F (2.3%, 1/44). Among these, 44.0% (11/25) were single genotype, 36.0% (9/25) were dual and 20.0% (5/25) were triple genotype. The most frequent dual combination was G/H (44.4%, 4/9), while triple-mixtures were H/G/D (60.0%, 3/5). The increase in the number of genotypes correlated positively with age (Spearman’s Rho = 0.53, p = 0.0069) and negatively with platelet levels (Spearman’s Rho = − 0.416, p = 0.039). HBV viral load was higher in triply-infected than dually infected (31623.0 IU/mL vs. 1479.0 IU/mL, p = 0.029) patients. Triple-mixed infection was associated with significant liver fibrosis (OR = 15.0 95%CI = 1.29 – 174.38, p = 0.027). In conclusion, infection with mixtures of HBV genotypes is frequent in HIV patients causing significant hepatic fibrosis related to high viral load, especially in triple genotype mixtures.
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Affiliation(s)
- Alexis Jose-Abrego
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Mexico.,Health Sciences Center, University of Guadalajara, Guadalajara, Mexico
| | - Sonia Roman
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Mexico.,Health Sciences Center, University of Guadalajara, Guadalajara, Mexico
| | - João Renato Rebello Pinho
- LIM-07, Department of Gastroenterology, School of Medicine, Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Arturo Panduro
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, "Fray Antonio Alcalde," Guadalajara, Mexico.,Health Sciences Center, University of Guadalajara, Guadalajara, Mexico
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26
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Novel Genetic Rearrangements in Hepatitis B Virus: Complex Structural Variations and Structural Variation Polymorphisms. Viruses 2021; 13:v13030473. [PMID: 33809245 PMCID: PMC8000817 DOI: 10.3390/v13030473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
Chronic hepatitis B virus (HBV) causes serious clinical problems, such as liver cirrhosis and hepatocellular carcinoma. Current antiviral treatments suppress HBV; however, the clinical cure rate remains low. Basic research on HBV is indispensable to eradicate and cure HBV. Genetic alterations are defined by nucleotide substitutions and canonical forms of structural variations (SVs), such as insertion, deletion and duplication. Additionally, genetic changes inconsistent with the canonical forms have been reported, and these have been termed complex SVs. Detailed analyses of HBV using bioinformatical applications have detected complex SVs in HBV genomes. Sequence gaps and low sequence similarity have been observed in the region containing complex SVs. Additionally, insertional motif sequences have been observed in HBV strains with complex SVs. Following the analyses of complex SVs in the HBV genome, the role of SVs in the genetic diversity of orthohepadnavirus has been investigated. SV polymorphisms have been detected in comparisons of several species of orthohepadnaviruses. As mentioned, complex SVs are composed of multiple SVs. On the contrary, SV polymorphisms are observed as insertions of different SVs. Up to a certain point, nucleotide substitutions cause genetic differences. However, at some point, the nucleotide sequences are split into several particular patterns. These SVs have been observed as polymorphic changes. Different species of orthohepadnaviruses possess SVs which are unique and specific to a certain host of the virus. Studies have shown that SVs play an important role in the HBV genome. Further studies are required to elucidate their virologic and clinical roles.
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27
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Glebe D, Goldmann N, Lauber C, Seitz S. HBV evolution and genetic variability: Impact on prevention, treatment and development of antivirals. Antiviral Res 2020; 186:104973. [PMID: 33166575 DOI: 10.1016/j.antiviral.2020.104973] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Hepatitis B virus (HBV) poses a major global health burden with 260 million people being chronically infected and 890,000 dying annually from complications in the course of the infection. HBV is a small enveloped virus with a reverse-transcribed DNA genome that infects hepatocytes and can cause acute and chronic infections of the liver. HBV is endemic in humans and apes representing the prototype member of the viral family Hepadnaviridae and can be divided into 10 genotypes. Hepadnaviruses have been found in all vertebrate classes and constitute an ancient viral family that descended from non-enveloped progenitors more than 360 million years ago. The de novo emergence of the envelope protein gene was accompanied with the liver-tropism and resulted in a tight virus-host association. The oldest HBV genomes so far have been isolated from human remains of the Bronze Age and the Neolithic (~7000 years before present). Despite the remarkable stability of the hepadnaviral genome over geological eras, HBV is able to rapidly evolve within an infected individual under pressure of the immune response or during antiviral treatment. Treatment with currently available antivirals blocking intracellular replication of HBV allows controlling of high viremia and improving liver health during long-term therapy of patients with chronic hepatitis B (CHB), but they are not sufficient to cure the disease. New therapy options that cover all HBV genotypes and emerging viral variants will have to be developed soon. In addition to the antiviral treatment of chronically infected patients, continued efforts to expand the global coverage of the currently available HBV vaccine will be one of the key factors for controlling the rising global spread of HBV. Certain improvements of the vaccine (e.g. inclusion of PreS domains) could counteract known problems such as low or no responsiveness of certain risk groups and waning anti-HBs titers leading to occult infections, especially with HBV genotypes E or F. But even with an optimal vaccine and a cure for hepatitis B, global eradication of HBV would be difficult to achieve because of an existing viral reservoir in primates and bats carrying closely related hepadnaviruses with zoonotic potential.
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Affiliation(s)
- Dieter Glebe
- Institute of Medical Virology, Justus Liebig University of Giessen, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Schubertstr. 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany.
| | - Nora Goldmann
- Institute of Medical Virology, Justus Liebig University of Giessen, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Schubertstr. 81, 35392, Giessen, Germany
| | - Chris Lauber
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany; Research Group Computational Virology, Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz Centre for Infection Research and the Hannover Medical School, Cluster of Excellence RESIST, Hannover Medical School, 30625, Hannover, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany; Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120, Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Sites Giessen, Heidelberg, Hannover, Germany.
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28
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Pujol F, Jaspe RC, Loureiro CL, Chemin I. Hepatitis B virus American genotypes: Pathogenic variants ? Clin Res Hepatol Gastroenterol 2020; 44:825-835. [PMID: 32553521 DOI: 10.1016/j.clinre.2020.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) chronic infection is responsible for almost 900.000 deaths each year, due to cirrhosis or hepatocellular carcinoma (HCC). Ten HBV genotypes have been described (A-J). HBV genotype F and H circulate in America. HBV genotypes have been further classified in subgenotypes. There is a strong correlation between the genetic admixture of the American continent and the frequency of genotypes F or H: a high frequency of these genotypes is found in countries with a population with a higher ratio of Amerindian to African genetic admixture. The frequency of occult HBV infection in Amerindian communities from Latin America seems to be higher than the one found in other HBV-infected groups, but its association with American genotypes is unknown. There is growing evidence that some genotypes might be associated with a faster evolution to HCC. In particular, HBV genotype F has been implicated in a frequent and rapid progression to HCC. However, HBV genotype H has been associated to a less severe progression of disease. This study reviews the diversity and frequency of autochthonous HBV variants in the Americas and evaluates their association to severe progression of disease. Although no significant differences were found in the methylation pattern between different genotypes and subgenotypes of the American types, basal core promoter mutations might be more frequent in some subgenotypes, such as F1b and F2, than in other American subgenotypes or genotype H. F1b and probably F2 may be associated with a severe presentation of liver disease as opposed to a more benign course for subgenotype F4 and genotype H. Thus, preliminary evidence suggests that not all of the American variants are associated with a rapid progression to HCC.
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Affiliation(s)
- Flor Pujol
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela.
| | - Rossana C Jaspe
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, CMBC, IVIC, Apdo 20632, Caracas 1020A, Venezuela
| | - Isabelle Chemin
- INSERM U1052, CNRS 5286, Université de Lyon, Université Claude Bernard Lyon 1, centre Léon Bérard, centre de recherche en cancérologie de Lyon, 69000, Lyon, France
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29
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Insights into the genetic diversity, recombination, and systemic infections with evidence of intracellular maturation of hepadnavirus in cats. PLoS One 2020; 15:e0241212. [PMID: 33095800 PMCID: PMC7584178 DOI: 10.1371/journal.pone.0241212] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV) is a human pathogen of global concern, while a high diversity of viruses related to HBV have been discovered in other animals during the last decade. Recently, the novel mammalian hepadnavirus, tentatively named domestic cat hepadnavirus (DCH), was detected in an immunocompromised cat. Herein, a collection of 209 cat sera and 15 hepato-diseased cats were screened for DCH using PCR, resulting in 12.4% and 20% positivity in the tested sera and necropsied cats, respectively. Among the DCH-positive sera, a significantly high level of co-detection with retroviral infection was found, with the highest proportion being co-detection with feline immunodeficiency virus (FIV). Full-length genome characterization of DCH revealed the genetic diversity between the nine Thai DCH sequences obtained, and that they phylogenetically formed three distinct monophyletic clades. A putative DCH recombinant strain was found, suggesting a possible role of recombination in DCH evolution. Additionally, quantitative PCR was used to determine the viral copy number in various organs of the DCH-moribund cats, while the pathological findings were compared to the viral localization in hepatocytes, adjacent to areas of hepatic fibrosis, by immunohistochemical (IHC) and western blot analysis. In addition to the liver, positive-DCH immunoreactivity was found in various other organs, including kidneys, lung, heart, intestine, brain, and lymph nodes, providing evidence of systemic infection. Ultrastructure of infected cells revealed electron-dense particles in the nucleus and cytoplasm of hepatocytes, bronchial epithelial cells, and fibroblasts. We propose the intracellular development mechanism of this virus. Although the definitive roles of pathogenicity of DCH remains undetermined, a contributory role of the virus associated with systemic diseases is possible.
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30
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The evolution and clinical impact of hepatitis B virus genome diversity. Nat Rev Gastroenterol Hepatol 2020; 17:618-634. [PMID: 32467580 DOI: 10.1038/s41575-020-0296-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 02/06/2023]
Abstract
The global burden of hepatitis B virus (HBV) is enormous, with 257 million persons chronically infected, resulting in more than 880,000 deaths per year worldwide. HBV exists as nine different genotypes, which differ in disease progression, natural history and response to therapy. HBV is an ancient virus, with the latest reports greatly expanding the host range of the Hepadnaviridae (to include fish and reptiles) and casting new light on the origins and evolution of this viral family. Although there is an effective preventive vaccine, there is no cure for chronic hepatitis B, largely owing to the persistence of a viral minichromosome that is not targeted by current therapies. HBV persistence is also facilitated through aberrant host immune responses, possibly due to the diverse intra-host viral populations that can respond to host-mounted and therapeutic selection pressures. This Review summarizes current knowledge on the influence of HBV diversity on disease progression and treatment response and the potential effect on new HBV therapies in the pipeline. The mechanisms by which HBV diversity can occur both within the individual host and at a population level are also discussed.
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31
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Gish RG. We Are All Africans: A Highly Personal Migratory View of the History of Hepatitis B. Clin Liver Dis (Hoboken) 2020; 16:24-33. [PMID: 33042524 PMCID: PMC7538925 DOI: 10.1002/cld.989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 02/04/2023] Open
Abstract
Watch an interview with the author.
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Affiliation(s)
- Robert G. Gish
- Robert G. Gish Consultants LLCLa JollaCA
- Medical Director, Hepatitis B FoundationDoylestownPA
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32
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Neukamm J, Pfrengle S, Molak M, Seitz A, Francken M, Eppenberger P, Avanzi C, Reiter E, Urban C, Welte B, Stockhammer PW, Teßmann B, Herbig A, Harvati K, Nieselt K, Krause J, Schuenemann VJ. 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC Biol 2020; 18:108. [PMID: 32859198 PMCID: PMC7456089 DOI: 10.1186/s12915-020-00839-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging. RESULTS The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed. CONCLUSIONS The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.
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Affiliation(s)
- Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Alexander Seitz
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Michael Francken
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Partick Eppenberger
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, USA
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Christian Urban
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Beatrix Welte
- Institute of Pre- and Protohistory and Medieval Archaeology, Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Philipp W Stockhammer
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799, Munich, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Barbara Teßmann
- Berlin Society of Anthropology, Ethnology and Prehistory, 10117, Berlin, Germany.,Museum of Prehistory and Early History, SMPK Berlin, 10117, Berlin, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Katerina Harvati
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,DFG Centre for Advanced Studies Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.
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33
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Datta S. Excavating new facts from ancient Hepatitis B virus sequences. Virology 2020; 549:89-99. [PMID: 32858309 DOI: 10.1016/j.virol.2020.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/02/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022]
Abstract
Recently, two independent studies discovered 15 ancient Hepatitis B virus (aHBV) sequences, of which 7 dated back to the Neolithic age (NA) and the Bronze Age (BA). In the present research, all the available aHBV sequences were collectively re-analysed with reference to extant HBV diversity to understand the role of these aHBV genotypes in evolution of extant HBV genetic diversity. Several intergenotype recombination events were documented, which corroborated well with population admixture and ancient human migration. Present analyses suggested replacement of HBV genotype associated with early Neolithic European farming cultures by the migrating steppe people, during Bronze Age Steppe migration. Additionally, detailed analyses of recombinations revealed evolution of a number of extant genotypes and suggested their possible site of origin. Through this manuscript, novel and important findings of the analyses are communicated.
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Affiliation(s)
- Sibnarayan Datta
- Molecular Virology Laboratory, Entomology & Biothreat Management Division, Defence Research Laboratory, Defence R&D Organization (DRDO), PO Bag 02, Tezpur HPO, Assam, 784001, India.
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34
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McNaughton AL, Revill PA, Littlejohn M, Matthews PC, Ansari MA. Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences. J Gen Virol 2020; 101:271-283. [PMID: 32134374 PMCID: PMC7416611 DOI: 10.1099/jgv.0.001387] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online (https://doi.org/10.6084/m9.figshare.8851946) as a simple open-access resource.
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Affiliation(s)
- Anna L. McNaughton
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Peter A. Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Philippa C. Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - M. Azim Ansari
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
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35
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Al-Qahtani AA, Pourkarim MR, Trovão NS, Vergote V, Li G, Thijssen M, Abdo AA, Sanai FM, Dela Cruz D, Bohol MFF, Al-Anazi MR, Al-Ahdal MN. Molecular epidemiology, phylogenetic analysis and genotype distribution of hepatitis B virus in Saudi Arabia: Predominance of genotype D1. INFECTION GENETICS AND EVOLUTION 2019; 77:104051. [PMID: 31634640 DOI: 10.1016/j.meegid.2019.104051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/28/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023]
Abstract
Despite the implementation of various vaccination programs, hepatitis B virus (HBV) poses a considerable health problem in Saudi Arabia. Insight on HBV evolutionary history in the region is limited. We performed a comprehensive epidemiological and phylogenetic reconstruction based on a large cohort of HBV infected patients. Three hundred and nineteen HBV-infected patients with different clinical manifestations, including inactive and active chronic carriers and patients with cirrhosis and hepatocellular carcinoma (HCC), were enrolled in this study. The full-length large S gene was amplified and sequenced. Phylogenetic analysis was performed to determine the genotype and subgenotypes of the isolates. Phylogenetic tree analysis revealed that genotype D is the most dominant genotype among patients. Moreover, this analysis identified two strains with genotype E isolated from active carriers. Detailed phylogenetic analyses confirmed the presence of four HBV D subgenotypes, D1 (93%, n = 296), D2 (0.02%, n = 5), D3 (0.003%, n = 1), and D4 (0.003%, n = 1). In addition, six genotype D strains were not assigned to any existing HBV D subgenotype. The large S gene of eight strains showed signatures of genotype recombination between the genotypes D and A and between D and E. Several strains harbored medically important point mutations at the protein level. Along with the dominance of the HBV genotype D, isolation of the E genotype and several recombinant strains from patients with Saudi Arabian origin is an essential result for decisions involving therapeutic measures for patients. Development of vaccines and detection of diagnostic escape mutations at antigenic epitopes on the HBsAg will be valuable to public health authorities. Furthermore, the diversity at the nucleotide and amino acid levels and different proportions of dN/dS at the PreS1, PreS2, and HBsAg reveal the selective pressure trend from inactive status towards advanced liver diseases.
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Affiliation(s)
- Ahmed A Al-Qahtani
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Department of Microbiology and Immunology, Alfaisal University, School of Medicine, Riyadh, Saudi Arabia.
| | - Mahmoud Reza Pourkarim
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Nídia Sequeira Trovão
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Guangdi Li
- Department of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Marijn Thijssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Ayman A Abdo
- Section of Gastroenterology, Department of Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Faisal M Sanai
- Gastroenterology Unit, Department of Medicine, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Damian Dela Cruz
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Marie Fe F Bohol
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mashael R Al-Anazi
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Mohammed N Al-Ahdal
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; Department of Microbiology and Immunology, Alfaisal University, School of Medicine, Riyadh, Saudi Arabia
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36
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Fujiwara K, Matsuura K, Matsunami K, Iio E, Nagura Y, Nojiri S, Kataoka H. Novel Genetic Rearrangements Termed "Structural Variation Polymorphisms" Contribute to the Genetic Diversity of Orthohepadnaviruses. Viruses 2019; 11:v11090871. [PMID: 31533314 PMCID: PMC6783994 DOI: 10.3390/v11090871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/08/2019] [Accepted: 09/17/2019] [Indexed: 12/27/2022] Open
Abstract
The genetic diversity of orthohepadnaviruses is not yet fully understood. This study was conducted to investigate the role of structural variations (SVs) in their diversity. Genetic sequences of orthohepadnaviruses were retrieved from databases. The positions of sequence gaps were investigated, since they were found to be related to SVs, and they were further used to search for SVs. Then, a combination of pair-wise and multiple alignment analyses was performed to analyze the genomic structure. Unique patterns of SVs were observed; genetic sequences at certain genomic positions could be separated into multiple patterns, such as no SV, SV pattern 1, SV pattern 2, and SV pattern 3, which were observed as polymorphic changes. We provisionally referred to these genetic changes as SV polymorphisms. Our data showed that higher frequency of sequence gaps and lower genetic identity were observed in the pre-S1-S2 region of various types of HBVs. Detailed examination of the genetic structure in the pre-S region by a combination of pair-wise and multiple alignment analyses showed that the genetic diversity of orthohepadnaviruses in the pre-S1 region could have been also induced by SV polymorphisms. Our data showed that novel genetic rearrangements provisionally termed SV polymorphisms were observed in various orthohepadnaviruses.
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Affiliation(s)
- Kei Fujiwara
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan.
| | - Kentaro Matsuura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan.
| | - Kayoko Matsunami
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan.
| | - Etsuko Iio
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan.
| | - Yoshihito Nagura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan.
| | - Shunsuke Nojiri
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan.
| | - Hiromi Kataoka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan.
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37
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Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F. Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses 2019; 11:E859. [PMID: 31540135 PMCID: PMC6784155 DOI: 10.3390/v11090859] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/15/2023] Open
Abstract
RNA recombination is a major driving force in the evolution and genetic architecture shaping of enteroviruses. In particular, intertypic recombination is implicated in the emergence of most pathogenic circulating vaccine-derived polioviruses, which have caused numerous outbreaks of paralytic poliomyelitis worldwide. Recent experimental studies that relied on recombination cellular systems mimicking natural genetic exchanges between enteroviruses provided new insights into the molecular mechanisms of enterovirus recombination and enabled to define a new model of genetic plasticity for enteroviruses. Homologous intertypic recombinant enteroviruses that were observed in nature would be the final products of a multi-step process, during which precursor nonhomologous recombinant genomes are generated through an initial inter-genomic RNA recombination event and can then evolve into a diversity of fitter homologous recombinant genomes over subsequent intra-genomic rearrangements. Moreover, these experimental studies demonstrated that the enterovirus genome could be defined as a combination of genomic modules that can be preferentially exchanged through recombination, and enabled defining the boundaries of these recombination modules. These results provided the first experimental evidence supporting the theoretical model of enterovirus modular evolution previously elaborated from phylogenetic studies of circulating enterovirus strains. This review summarizes our current knowledge regarding the mechanisms of recombination in enteroviruses and presents a new evolutionary process that may apply to other RNA viruses.
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Affiliation(s)
- Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de las Américas, Quito EC170125, Pichincha, Ecuador.
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Maël Bessaud
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Bruno Blondel
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
| | - Francis Delpeyroux
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
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38
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Yuen LKW, Littlejohn M, Duchêne S, Edwards R, Bukulatjpi S, Binks P, Jackson K, Davies J, Davis JS, Tong SYC, Locarnini S. Tracing Ancient Human Migrations into Sahul Using Hepatitis B Virus Genomes. Mol Biol Evol 2019; 36:942-954. [PMID: 30856252 DOI: 10.1093/molbev/msz021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The entry point and timing of ancient human migration into continental Sahul (the combined landmass of Australia, New Guinea, and Tasmania) are subject to debate. Unique strains of hepatitis B virus (HBV) are endemic among modern-day Australian Aboriginals (HBV/C4) and Indigenous Melanesians (HBV/C3). We postulated that HBV genomes could be used to infer human population movements because the main HBV transmission route in endemic populations is via mother-to-child for genotypes B and C infections. Phylogenetic and phylogeographic analyses of HBV genomes inferred the origin of HBV/C4 to be >59 thousand years ago (ka) (95% HPD: 34-85 ka), and most likely to have occurred on the Sunda Shelf (southeast extension of the continental shelf of Southeast Asia). Our analysis further suggested an age of >51 ka (95% Highest Posterior Density (HPD): 36-67 ka) for the most recent common ancestor of HBV/C4 in Australia, correlating with the arrival time of anatomically modern humans into Australia, with the entry point suggested along a southern route via Timor. While we also inferred the origin of HBC/C3 to be on the Sunda Shelf, our analyses suggested that it was carried into Melanesia by Indigenous Melanesians who migrated through New Guinea north of the highlands. These findings reveal that HBV genomes can be used to infer ancient human population movements.
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Affiliation(s)
- Lilly K W Yuen
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Rosalind Edwards
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Sarah Bukulatjpi
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Ngalkanbuy Clinic, Galiwin'ku, Australia
| | - Paula Binks
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Kathy Jackson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Jane Davies
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Australia
| | - Joshua S Davis
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,John Hunter Hospital, Newcastle, Australia
| | - Steven Y C Tong
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.,Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Australia.,Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
| | - Stephen Locarnini
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at the Doherty Institute, Melbourne, Australia
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39
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Ren CC, Chen QY, Wang XY, Harrison TJ, Yang QL, Hu LP, Liu HB, He X, Jia HH, Fang ZL. Novel subgenotype D11 of hepatitis B virus in NaPo County, Guangxi, bordering Vietnam. J Gen Virol 2019; 100:828-837. [PMID: 30990399 DOI: 10.1099/jgv.0.001257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus has been classified into 10 genotypes and 48 subgenotypes worldwide. We found previously, through polymerase chain reaction (PCR) amplification of a sample collected in 2011, that an HBsAg carrier was infected with two genotypes (B and D) of HBV. We carried out cloning, sequencing and phylogenetic analysis of the complete genomes and, for confirmation, analysed a sample collected from the same individual in 2018. Fifteen complete sequences were obtained from each sample. The carrier was infected in 2011 by genotypes B and D and by various recombinants, but only genotype D was present in 2018. The major and minor parents of the recombinants are genotypes B and D, respectively, although the recombination breakpoints vary among them. All 23 genotype D isolates form a cluster, branching out from other subgenotype D sequences and supported by a 100 % bootstrap value. Based on complete genome sequences, almost all of the estimated intragroup nucleotide divergence values between our isolates and HBV subgenotypes D1-D10 exceed 4 %. Compared to the other subgenotypes (D1-D10), 35 unique amino acids were present in our isolates. Our data provide evidence for a novel subgenotype, provisionally designated HBV subgenotype D11.
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Affiliation(s)
- Chuang-Chuang Ren
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China.,2School of Preclinical Medicine, Guangxi Medical University, UCL Medical School, 22 ShuangYong Road Nanning, Guangxi 530021, PR China
| | - Qin-Yan Chen
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
| | - Xue-Yan Wang
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
| | | | - Qing-Li Yang
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
| | - Li-Ping Hu
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
| | - Hua-Bing Liu
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China.,2School of Preclinical Medicine, Guangxi Medical University, UCL Medical School, 22 ShuangYong Road Nanning, Guangxi 530021, PR China
| | - Xiang He
- 4Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, PR China
| | - Hui-Hua Jia
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China.,2School of Preclinical Medicine, Guangxi Medical University, UCL Medical School, 22 ShuangYong Road Nanning, Guangxi 530021, PR China
| | - Zhong-Liao Fang
- 1Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, PR China
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40
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Ababneh NA, Sallam M, Kaddomi D, Attili AM, Bsisu I, Khamees N, Khatib A, Mahafzah A. Patterns of hepatitis B virus S gene escape mutants and reverse transcriptase mutations among genotype D isolates in Jordan. PeerJ 2019; 7:e6583. [PMID: 30867996 PMCID: PMC6410685 DOI: 10.7717/peerj.6583] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/08/2019] [Indexed: 12/18/2022] Open
Abstract
Background Hepatitis B virus (HBV) is an important infectious cause of morbidity and mortality in Jordan. HBV genotype D is the most prevalent in the country. Virus escape mutants in the HBV S region is an important public health problem halting preventive efforts. The aim of the current study was to investigate patterns of HBV escape and resistance mutations and to assess domestic transmission of the virus. Methods Patients infected with HBV were recruited at Jordan University Hospital (n = 56) and were diagnosed during (1984-2012). A total of 37 partial HBV S sequences were generated using Sanger's method. Mutation analysis was done using the HIV grade HBV drug resistance interpretation online tool and Geno2pheno (HBV) online tools. Domestic transmission of HBV was assessed using maximum likelihood phylogenetic inference with similar GenBank sequences. Results Genotyping revealed an exclusive presence of sub-genotype D1. Typical HBV escape mutants were identified in seven patients. These mutations included: L109R, Q129R, M133L, S143L and D144E with overall prevalence of 18.9% (95% CI [9.5-34.2]). Reverse transcriptase (RT) sequence analysis showed mutations in three patients with overall prevalence of 8.1% (95% CI [2.8-21.3]). RT mutations included: V173L, S202I, L180M, M204V and T184A. Transmission cluster analysis revealed a relatively high proportion of infections taking place as a result of domestic spread (29.7%). Conclusions Based on our findings, RT mutation analysis appears to be of high value before the initiation of therapy in patients with chronic HBV infection in Jordan. Phylogenetic analyses revealed a considerable proportion of local spread in the country which should be considered in the preventive infection control efforts.
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Affiliation(s)
- Nidaa A Ababneh
- Cell Therapy Center (CTC), University of Jordan, Amman, Jordan
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan.,Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Doaa Kaddomi
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, Jordan
| | | | - Isam Bsisu
- School of Medicine, University of Jordan, Amman, Jordan
| | - Nadia Khamees
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, Jordan
| | - Amer Khatib
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, Jordan
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
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41
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Catanach TA, Sweet AD, Nguyen NPD, Peery RM, Debevec AH, Thomer AK, Owings AC, Boyd BM, Katz AD, Soto-Adames FN, Allen JM. Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ 2019; 7:e6142. [PMID: 30627489 PMCID: PMC6321758 DOI: 10.7717/peerj.6142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 11/14/2018] [Indexed: 01/05/2023] Open
Abstract
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected "by eye" prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.
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Affiliation(s)
- Therese A. Catanach
- Ornithology Department, Academy of Natural Sciences of Drexel University, Philadelphia, PA, United States of America
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Andrew D. Sweet
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Nam-phuong D. Nguyen
- Computer Science and Engineering, University of San Diego, California, La Jolla, CA, United States of America
| | - Rhiannon M. Peery
- Department of Biology, University of Alberta, Edmonton, Alberta, Canada
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Andrew H. Debevec
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Andrea K. Thomer
- School of Information, University of Michigan—Ann Arbor, Ann Arbor, MI, United States of America
| | - Amanda C. Owings
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Bret M. Boyd
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, University of Georga, Athens, GA, United States of America
| | - Aron D. Katz
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Felipe N. Soto-Adames
- Florida State Collection of Arthropods, Florida Department of Agriculture and Consumer Services, Gainesville, FL, United States of America
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America
| | - Julie M. Allen
- Biology Department, University of Nevada, Reno, Reno, NV, United States of America
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42
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Jia L, Hu F, Li H, Li L, Tang X, Liu Y, Deng H, Han J, Li J, Cai W. Characterization of small genomic regions of the hepatitis B virus should be performed with more caution. Virol J 2018; 15:188. [PMID: 30526629 PMCID: PMC6288937 DOI: 10.1186/s12985-018-1100-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/26/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Hepatitis B virus is a hepatotropic DNA virus that reproduces via an RNA intermediate. It can lead to an increased risk of serious liver diseases such as hepatocellular carcinoma and is a serious threat to public health. Currently, the HBV are designated based on greater than 8% nucleotide variation along the whole genome. The recombination of HBV is very common, a large majority of which are recombinants between 2 genotypes. The current work aims to characterize a suspected recombinant involving 3 genotypes. METHODS Fifty-seven HBV full-genome sequences were obtained from 57 patients co-infected with HBV and HIV-1 by amplification coupled with sequencing. JpHMM and RDP4 were used to perform recombination analysis respectively. The recombination results of a suspected 3-genotypic recombinant were further confirmed by both maximum likelihood phylogenetic tree and Mrbayes tree. RESULTS JpHMM recombination analysis clearly indicated one 3-genotypic HBV recombinant composing of B/C/D. The genotype assignments are supported by significant posterior probabilities. The subsequent phylogenetic analysis of sub-regions derived from inferred breakpoints led to a disagreement on the assignment of D segment. Investigating the conflict, further exploration by RDP4 and phylogenies revealed that the jpHMM-derived 3-genotypic recombinant is actually a B/C genotypic recombinant with C fragment spanning 1899 to 2295 (jpHMM) or 1821 to 2199 (RDP4). CONCLUSIONS The whole analysis indicated that (i) determination of small genomic regions should be performed with more caution, (ii) combinations of various recombination detection approaches conduce to obtain impartial results, and (iii) a unified system of nomenclature of HBV genotypes is necessary.
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Affiliation(s)
- Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Fengyu Hu
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510060 Guangdong China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Xiaoping Tang
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510060 Guangdong China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Haohui Deng
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510060 Guangdong China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Weiping Cai
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510060 Guangdong China
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43
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Fujiwara K, Matsuura K, Matsunami K, Iio E, Nojiri S. Characterization of hepatitis B virus with complex structural variations. BMC Microbiol 2018; 18:202. [PMID: 30509169 PMCID: PMC6276219 DOI: 10.1186/s12866-018-1350-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 11/20/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is one of the most serious public health issues. Recent HBV genetic research has revealed novel genetic rearrangements termed complex structural variations (SVs), which are composed of combinations of SVs such as insertions, deletions, and duplications. An extensive search was made for complex SVs of HBV and their characteristics were analyzed. RESULTS Fifty-five HBV strains with complex SVs were identified by analyzing genetic sequences of HBV with bioinformatical tools. Along with 15 HBV strains with complex SVs in a previous report, a total of 70 HBV strains harboring complex SVs were analyzed. Complex SVs in the HBV genome were located frequently between nt 1500 and 2000. Insertions were observed in 65/70 (92.9%) of HBV strains with complex SVs. As insertional motif sequences, hepatocyte nuclear factor 1 binding site, a sequence complementary to part of box α in enhancer II, and insertions of unknown origins were observed. The complex SVs were classified into six groups, and combination of insertion and deletion was observed more frequently than other patterns. CONCLUSION Through an extensive search of HBV sequences, new strains with complex SVs were identified in this study. Characteristics of HBV with complex SVs were clarified by the analysis of 70 HBV strains harboring complex SVs. Further investigation is required to elucidate its role in pathogenesis of HBV-related liver disease.
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Affiliation(s)
- Kei Fujiwara
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho, Nagoya, Aichi, 467-8601, Japan.
| | - Kentaro Matsuura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho, Nagoya, Aichi, 467-8601, Japan
| | - Kayoko Matsunami
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho, Nagoya, Aichi, 467-8601, Japan
| | - Etsuko Iio
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho, Nagoya, Aichi, 467-8601, Japan
| | - Shunsuke Nojiri
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho, Nagoya, Aichi, 467-8601, Japan
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44
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Kramvis A, Kostaki EG, Hatzakis A, Paraskevis D. Immunomodulatory Function of HBeAg Related to Short-Sighted Evolution, Transmissibility, and Clinical Manifestation of Hepatitis B Virus. Front Microbiol 2018; 9:2521. [PMID: 30405578 PMCID: PMC6207641 DOI: 10.3389/fmicb.2018.02521] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/03/2018] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) infection, a global public health problem can be asymptomatic, acute or chronic and can lead to serious consequences of infection, including cirrhosis, and hepatocellular carcinoma. HBV, a partially double stranded DNA virus, belongs to the family Hepadnaviridae, and replicates via reverse transcription of an RNA intermediate. This reverse transcription is catalyzed by a virus-encoded polymerase that lacks proof reading ability, which leads to sequence heterogeneity. HBV is classified into nine genotypes and at least 35 subgenotypes, which may be characterized by distinct geographical distributions. This HBV diversification and distinct geographical distribution has been proposed to be the result of the co-expansion of HBV with modern humans, after their out-of-Africa migration. HBeAg is a non-particulate protein of HBV that has immunomodulatory properties as a tolerogen that allows the virus to establish HBV infection in vivo. During the natural course of infection, there is seroconversion from a HBeAg-positive phase to a HBeAg-negative, anti-HBe-positive phase. During this seroconversion, there is loss of tolerance to infection and immune escape-HBeAg-negative mutants can be selected in response to the host immune response. The different genotypes and, in some cases, subgenotypes develop different mutations that can affect HBeAg expression at the transcriptional, translational and post-translational levels. The ability to develop mutations, affecting HBeAg expression, can influence the length of the HBeAg-positive phase, which is important in determining both the mode of transmission and the clinical course of HBV infection. Thus, the different genotypes/subgenotypes have evolved in such a way that they exhibit different modes of transmission and clinical manifestation of infection. Loss of HBeAg may be a sign of short-sighted evolution because there is loss of tolerogenic ability of HBeAg and HBeAg-negative virions are less transmissible. Depending on their ability to lead to HBeAg seroconversion, the genotype/subgenotypes exhibit varying degrees of short-sighted evolution. The “arms race” between HBV and the immune response to HBeAg is multifaceted and its elucidation intricate, with transmissibility and persistence being important for the survival of the virus. We attempt to shed some light on this complex interplay between host and virus.
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Affiliation(s)
- Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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45
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Kmet Lunaček N, Poljak M, Matičič M. Distribution of hepatitis B virus genotypes in Europe and clinical implications: a review. ACTA DERMATOVENEROLOGICA ALPINA PANNONICA ET ADRIATICA 2018. [DOI: 10.15570/actaapa.2018.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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46
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Kostaki EG, Karamitros T, Stefanou G, Mamais I, Angelis K, Hatzakis A, Kramvis A, Paraskevis D. Unravelling the history of hepatitis B virus genotypes A and D infection using a full-genome phylogenetic and phylogeographic approach. eLife 2018; 7:36709. [PMID: 30082021 PMCID: PMC6118819 DOI: 10.7554/elife.36709] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/28/2018] [Indexed: 12/17/2022] Open
Abstract
Hepatitis B virus (HBV) infection constitutes a global public health problem. In order to establish how HBV was disseminated across different geographic regions, we estimated the levels of regional clustering for genotypes D and A. We used 916 HBV-D and 493 HBV-A full-length sequences to reconstruct their global phylogeny. Phylogeographic analysis was conducted by the reconstruction of ancestral states using the criterion of parsimony. The putative origin of genotype D was in North Africa/Middle East. HBV-D sequences form low levels of regional clustering for the Middle East and Southern Europe. In contrast, HBV-A sequences form two major clusters, the first including sequences mostly from sub-Saharan Africa, and the second including sequences mostly from Western and Central Europe. Conclusion: We observed considerable differences in the global dissemination patterns of HBV-D and HBV-A and different levels of monophyletic clustering in relation to the regions of prevalence of each genotype.
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Affiliation(s)
- Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| | - Timokratis Karamitros
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
| | - Garyfallia Stefanou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| | - Ioannis Mamais
- Department of Health Sciences, School of SciencesEuropean University of CyprusNicosiaCyprus
| | - Konstantinos Angelis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, Department of Internal Medicine, Faculty of Health ScienceUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical SchoolNational and Kapodistrian University of AthensAthensGreece
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47
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Shaha M, Hadisur Rahman M, Jahan M, Dey SK, Das KC, Hashem A, Salimullah M. Identification of a novel tri-genotypic recombinant Hepatitis B virus in Bangladesh. Virus Res 2018; 255:154-156. [PMID: 30040979 DOI: 10.1016/j.virusres.2018.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023]
Abstract
We report a novel tri-genotypic recombinant Hepatitis B virus (HBV) strain circulating in Bangladesh. The strain is recombinant with the genotypes D, C and E, of which, genotype E was not reported before in Bangladesh. Additionally, the complete genome has a frameshift deletion of nine nucleotides from overlapping Surface and Polymerase genes, and a vaccine escape mutation, A128 V, in the surface protein. This is the first report with such unusual recombination event responsible for rapid liver cirrhosis in a 13 year old patient in Bangladesh. This report may alert the clinicians to take the measure to prevent an upcoming outbreak of recombinant HBV.
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Affiliation(s)
- Modhusudon Shaha
- Microbial Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, 1349, Bangladesh
| | - Md Hadisur Rahman
- Molecular Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, 1349, Bangladesh
| | - Munira Jahan
- Department of Virology, Bangabandhu Sheikh Mujib Medical University, Dhaka, 1000, Bangladesh
| | - Shuvra Kanti Dey
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, 1349, Bangladesh
| | - Abu Hashem
- Microbial Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, 1349, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, 1349, Bangladesh.
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48
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Krause-Kyora B, Susat J, Key FM, Kühnert D, Bosse E, Immel A, Rinne C, Kornell SC, Yepes D, Franzenburg S, Heyne HO, Meier T, Lösch S, Meller H, Friederich S, Nicklisch N, Alt KW, Schreiber S, Tholey A, Herbig A, Nebel A, Krause J. Neolithic and medieval virus genomes reveal complex evolution of hepatitis B. eLife 2018; 7:36666. [PMID: 29745896 PMCID: PMC6008052 DOI: 10.7554/elife.36666] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022] Open
Abstract
The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genome by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results demonstrated that HBV has circulated in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. The ancient viruses appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.
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Affiliation(s)
- Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Jena, Germany.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Esther Bosse
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.,Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Alexander Immel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Christoph Rinne
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | | | - Diego Yepes
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Henrike O Heyne
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, United States.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, United States.,Program in Medical and Population Genetics, Broad Institute of MIT & Harvard, Cambridge, United States
| | - Thomas Meier
- Institute for Pre- and Protohistory and Near Eastern Archaeology, Heidelberg University, Heidelberg, Germany.,Heidelberg Center for the Environment, Heidelberg University, Heidelberg, Germany
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany
| | - Nicole Nicklisch
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany.,Danube Private University, Krems, Austria
| | - Kurt W Alt
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany.,Danube Private University, Krems, Austria.,Department of Biomedical Engineering, University Hospital Basel, University of Basel, Basel, Switzerland.,Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.,Clinic for Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
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49
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Mühlemann B, Jones TC, Damgaard PDB, Allentoft ME, Shevnina I, Logvin A, Usmanova E, Panyushkina IP, Boldgiv B, Bazartseren T, Tashbaeva K, Merz V, Lau N, Smrčka V, Voyakin D, Kitov E, Epimakhov A, Pokutta D, Vicze M, Price TD, Moiseyev V, Hansen AJ, Orlando L, Rasmussen S, Sikora M, Vinner L, Osterhaus ADME, Smith DJ, Glebe D, Fouchier RAM, Drosten C, Sjögren KG, Kristiansen K, Willerslev E. Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature 2018; 557:418-423. [PMID: 29743673 DOI: 10.1038/s41586-018-0097-z] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 04/06/2018] [Indexed: 12/16/2022]
Abstract
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
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Affiliation(s)
- Barbara Mühlemann
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Terry C Jones
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.,Institute of Virology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Irina Shevnina
- Archaeological Laboratory, Faculty of History and Law, A. A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Andrey Logvin
- Archaeological Laboratory, Faculty of History and Law, A. A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Emma Usmanova
- Saryarka Archaeological Institute, Karaganda State University, Karaganda, Kazakhstan
| | | | - Bazartseren Boldgiv
- Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tsevel Bazartseren
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, Mongolia
| | | | - Victor Merz
- Pavlodar State University, Pavlodar, Kazakhstan
| | - Nina Lau
- Centre for Baltic and Scandinavian Archaeology, Schleswig, Germany
| | - Václav Smrčka
- Institute for History of Medicine and Foreign Languages of the First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Egor Kitov
- N. N. Miklouho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Epimakhov
- South Ural Department, Institute of History and Archaeology UBRAS, South Ural State University, Chelyabinsk, Russia
| | - Dalia Pokutta
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - T Douglas Price
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Vyacheslav Moiseyev
- Department of Physical Anthropology, Peter the Great Museum of Anthropology and Ethnography, Saint-Petersburg, Russia
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Albert D M E Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Dieter Glebe
- Institute of Medical Virology, Justus Liebig University of Giessen, Giessen, Germany.,National Reference Centre for Hepatitis B and D Viruses, German Center for Infection Research (DZIF), Giessen, Germany
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Christian Drosten
- Institute of Virology, Charité, Universitätsmedizin Berlin, Berlin, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | | | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark. .,Cambridge GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Trust Sanger Institute, Hinxton, UK.
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Choi YM, Lee SY, Kim BJ. Naturally occurring hepatitis B virus reverse transcriptase mutations related to potential antiviral drug resistance and liver disease progression. World J Gastroenterol 2018; 24:1708-1724. [PMID: 29713126 PMCID: PMC5922991 DOI: 10.3748/wjg.v24.i16.1708] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/10/2018] [Accepted: 04/15/2018] [Indexed: 02/06/2023] Open
Abstract
The annual number of deaths caused by hepatitis B virus (HBV)-related disease, including cirrhosis and hepatocellular carcinoma (HCC), is estimated as 887000. The reported prevalence of HBV reverse transcriptase (RT) mutation prior to treatment is varied and the impact of preexisting mutations on the treatment of naïve patients remains controversial, and primarily depends on geographic factors, HBV genotypes, HBeAg serostatus, HBV viral loads, disease progression, intergenotypic recombination and co-infection with HIV. Different sensitivity of detection methodology used could also affect their prevalence results. Several genotype-dependent HBV RT positions that can affect the emergence of drug resistance have also been reported. Eight mutations in RT (rtL80I, rtD134N, rtN139K/T/H, rtY141F, rtM204I/V, rtF221Y, rtI224V, and rtM309K) are significantly associated with HCC progression. HBeAg-negative status, low viral load, and genotype C infection are significantly related to a higher frequency and prevalence of preexisting RT mutations. Preexisting mutations are most frequently found in the A-B interdomain of RT which overlaps with the HBsAg “a” determinant region, mutations of which can lead to simultaneous viral immune escape. In conclusion, the presence of baseline RT mutations can affect drug treatment outcomes and disease progression in HBV-infected populations via modulation of viral fitness and host-immune responses.
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Affiliation(s)
- Yu-Min Choi
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
| | - So-Young Lee
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
| | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute and Cancer Research Institute, Seoul National University, College of Medicine, Seoul 110799, South Korea
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